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Discussion Starter · #1 · (Edited)
So I had to pull my wife's transmission again (2007 Jeep Patriot 4x4 5 speed manual 2.4L). I pulled it about 18 months ago to change the slave cylinder. I posted some info then, and I'm just going to update now since I feel like I did a better job the second time around.


I pulled the transmission this time because it was leaking ATF fluid between the transaxle and PTU. There are two o-rings between the transaxle and PTU. I isolated all the leaks over the course of several days and when I was confident it was leaking at this location, I decided to pull the tranny again and replace the o-rings. The C/V axle seals were also leaking (although those can be changed without pulling the tranny).


Some of this is a repeat of my previous post, but I did things in a slightly different order this time with improved results.


First I disconnected and removed the battery. This required removing the airbox, etc. Airbox comes off by two twist knobs to remove air intake tube. Then I removed the large hose clamp from the airbox, unclamped the two sides, and removed them by pulling up and out. Then I removed the battery terminal connections and battery hold down bar (all 10mm). Next came the battery tray (which has four bolts and a nut holding it, 13mm).

Unbolted the computer so I can pull it up and out of the way. Removed the bracket that holds computer (2 bolts, one nut, or something like that).

I removed the shifter cables. Squeezed the plastic retainers together to slide them out of the keepers then pry up to pop the ball and socket joint apart. Unbolted the bracket that held the cables (3 bolts) from the tranny (it was in my way later removing an engine to transaxle bolt). Removed an electrical plug connection from the front (radiator) side of the transaxle.

Disconnected the hydraulic line that runs from the slave cylinder in the tranny to the clutch master cylinder. The fittings disconnect by gently pulling the metal clip until it slides out partially. Then the tubes pull apart. I removed all the holders and clips, then used a zip tie to hold the shifter cables and the hydraulic line out of the way.

Then I loosened the lug nuts. Then I jacked it up and put it on jackstands. Removed the wheels. Drained the transmission fluid into a pan (8mm allen wrench for the drain plug, couldn't fit my 8mm hex socket in the space available).

Remove the nut and bolt holding each lower ball joint together (18mm). This time I did NOT disconnect the tie rod ends or the sway bar. I was able to push the lower control arm down as I pulled the hub assembly out and back to separate them. I had to use a long pipe on one side but the other side came off easy.

Removed the cotter pin from the end of the cv axle and removed the metal washer and keeper. This time I had a cordless impact gun to remove the cv axle nut (1 1/4 inch worked correctly on the nut; don't know the metric equivalent).

This time both CV axles came out the hub pretty easy. Once the outer end was free on each cv axle, I pried the inner end out of the tranny on each side. Be careful where you pry, of course.
At this point I removed the PTU. There were 6 14mm bolts holding it (5 are all in the same plane, one is significantly longer--this one was also very stuck this time. used some spray penetrant and impact to remove it). Three of the shorter bolts are easily removed from the bottom. One of the top two short bolts had to be taken out from the top. The second top bolt was easier to access from the passenger wheel well with a lot of extensions. The long bolt was also accessible from the passenger wheel well.

The PTU and transaxle separated easily this time. The large o-ring had a 1 cm tear on the bottom; the torn piece was still present but separated and flattened. I suppose I tore it during reassembly (last time I installed it on the transaxle and then mounted them both to the motor; this time I installed the transaxle and then mounted to PTU last.)

Next I loosened all of the transaxle to engine bolts.

The starter has two 15mm bolts holding it onto the bellhousing (at the top of transaxle towards the front/radiator side). There was also a 13mm bolt near the starter that was holding on part of the air assembly. There were two 14mm transaxle to engine bolts on the top as well.

There were a number of transaxle to engine mounting bolts accessible from underneath the car. 5 or 6 visible from under the front bumper. There is one that is very difficult to reach that I didn't re-install last time. By removing the PTU first, this bolt would be easier to access, but still pretty difficult so I left it out again (I did find the bolt in the garage--- yay for being a packrat and keeping everything). For those of you doing it the first time, remove the PTU first and then its much easier. Otherwise, the PTU is in the way. You have to use a 14mm shallow well socket with a pivot adapter and a short extension. With a small pipe over the 3/8 ratchet we were able to break it loose and then remove it using our fingers (very slowly). I left the rest installed at this point but broke loose. (One actually broke this time; I used never-seize when I put it all back together to try and prevent losing anymore if I have to remove the tranny again).

Next there were three drivetrain mounts, one in the back (between drivetrain and firewall), one at the front (between the drivetrain and front bumper) and one at the drivers side end of the tranny at the top of the drivers wheel well.

I put a jack under the engine oil pan (with a piece of plywood on it to prevent damage to the pan). The rear bracket bolt is hard to access (16mm); once again the easiest way is through the passenger wheel well. The nut is held onto the bracket by a "keeper nut" although it may fall off if bumped. The front mount bolt is easier to access, but the bolt is welded to the bracket, so it won't turn no matter how hard you try; so make sure you put the ratchet on the bolt! The bar going under the drivetrain is held on by 2 15mm at the front and a short 18mm at the rear. I removed the front mount bracket from the transaxle to give me more room later when removing it from under the car (2 18mm I think). The top mount bolt is easy to access. I also removed the top mount bracket (3 18mm bolts) to give me more clearance for removing transaxle from under vehicle.

With the plastic cover removed from the 'front' (facing engine) section of the transmission bellhousing, it was possible to see the modular clutch to flywheel bolts. They are an 18mm. I had to put a socket on the crankshaft bolt (22mm) to turn the engine so that I could find each of those 4 bolts. A breaker bar on the crank bolt allowed us to hold everything still while we broke these four bolts free and removed them.

Then I put my tranny jack under the transaxle and completely removed the transaxle to engine bolts. A gentle 'shove' and my transmission disconnected completely onto the jack, and I lowered it and pulled it out from under the car.

Last time, I removed transaxle to replace the slave cylinder, which was held on by two bolts (10mm). Had to disconnect it from the short pipe with the bleeder valve (that passes thru bellhousing) by pulling the metal clip partially out and pulling the pipes apart. Then bolted up new slave cylinder and popped hydraulic lines back together and pushed metal clip back in till it snapped in place. I went ahead and put in a new modular clutch as well (too much work to have to do again anytime soon; original clutch had 132,000 miles).

I replaced the Drivers side CV axle seal (0518 9989 AA) while the transaxle was out. I bought a seal removal tool (never had one before, it worked way! better than a screwdriver and was only $8 at Harbor Freight). Also bought a $16 seal install set and the new seal popped right in.

I didn't have so much luck with the passenger side seal (6800 5623 AA). On this 4wd the passenger side seal is in the PTU. I tried installing it while transaxle was still out, but couldn't get it in. Perhaps if I had waited until the PTU was mounted to the transaxle and everything was solid and not moving maybe it would have went in easier. I actually ended up just putting the old seal back in, because it would go (the new one just wouldn't fit). This seal wasn't really leaking to begin with (maybe a drip or two, but most of my leaks were orings and drivers side cv axle seal).

There are two o=rings between the PTU and transaxle. No one could find a part number for the small one, so I used the closest match I had in a Viton oring kit I had previously bought (also at harbor freight). I got a new large oring from the Jeep dealership (6800 5267 AA). I put a little Vaseline on each one to hold it in place and help everything slide together. I put them onto the PTU while the transaxle was out so I had room to work, then I sat the PTU aside and installed the transaxle.

I cleaned out the bellhousing. I lubricated all the bolts with never-seize and then ran the bolts into all the holes while the transaxle was still out and assessible. If I had had the right size tap and die, I would have gone over all the threads with that, but I didn't so cleaned everything up with a wire wheel. I rolled the transaxle back under the car, jacked it into position. It is difficult to the rear mount lined up right, but the transmission jack makes the job a lot better. I got the transaxle to engine bolts started and snug. Then I put the four flywheel to modular clutch bolts back in (had to turn the crank again).

The PTU lined up and slid together easy onto the transaxle this time. Got all the bolts started and snugged.

The rest of re-assembly was pretty much reverse of removal. Nothing special, just make sure to tighten all the bolts and use torque wrench when possible.

I bled the clutch hydraulics by opening the bleeder at the bellhousing while my helper kept the master cylinder reservoir topped off. The pedal still felt soft, so I closed everything and I pumped the pedal a bunch of times (50 to 100 times) and then bled it again. Got more air out. Let it sit overnight, and repeated. After the 3rd time, clutch feels decent. I'll probably try bleeding again after a week of driving to remove any more air that may be in the system. Filled the tranny with ATF+4, about 3 quarts give or take. I replaced the two rubber plugs with new ones (much more pliable than the old ones, and only 5 bucks each).

Spent about $100 bucks on seals this time (dealership parts prices; no parts store could find the right seals). But the labor was cheap!

Removal and installation took a total of less than 8 hours. Removed one evening and re-installed the next day. Removed by myself, but had help with raising the transaxle back up. It would be possible but REALLY hard to line up the engine and transaxle without an extra set of hands.

So I should have replaced the seals last time, but couldn't find the parts anywhere (even the dealership had to order them for me this time; they didn't have them on hand). And it was my fault the oring was damaged. But I learned a little something last time and that made it easier the second time. It was 28,000 miles and 18 months inbetween the two removals. Vehicle now has 169,000 miles on it.

The good news is the main leaks are gone! I was putting a half a quart of ATF-4 in a week (she drives a lot for work). Wouldn't be so bad if the tranny fill was easier to get to---BUT its a PITA, so glad I won't be doing that so much anymore.

Still have a small drip from the passenger side CV axle seal. I'm going to order another new seal and try again to install it with transaxle in place (maybe it will be easier without the PTU flopping around).

Once again, I hope someone finds this useful. I actually looked up my last post to remind myself before doing the job this time!
 

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So just wondering why it was necessary to pull the whole transmission to repair a seal between the PTU and the transmission? I have a leak between my CVT and the PTU, so I was thinking all I needed to do was pull the PTU and replace the seals?
 

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The instructions for pulling the ptu say there are 6 bolts around the perimeter three on the bottom and three on the top. The center hole was empty on the top (on mine) did not find a long bolt maybe I missed one because I can't get it to separate.
 

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So I had to pull my wife's transmission again (2007 Jeep Patriot 4x4 5 speed manual 2.4L). I pulled it about 18 months ago to change the slave cylinder. I posted some info then, and I'm just going to update now since I feel like I did a better job the second time around.


I pulled the transmission this time because it was leaking ATF fluid between the transaxle and PTU. There are two o-rings between the transaxle and PTU. I isolated all the leaks over the course of several days and when I was confident it was leaking at this location, I decided to pull the tranny again and replace the o-rings. The C/V axle seals were also leaking (although those can be changed without pulling the tranny).


Some of this is a repeat of my previous post, but I did things in a slightly different order this time with improved results.


First I disconnected and removed the battery. This required removing the airbox, etc. Airbox comes off by two twist knobs to remove air intake tube. Then I removed the large hose clamp from the airbox, unclamped the two sides, and removed them by pulling up and out. Then I removed the battery terminal connections and battery hold down bar (all 10mm). Next came the battery tray (which has four bolts and a nut holding it, 13mm).

Unbolted the computer so I can pull it up and out of the way. Removed the bracket that holds computer (2 bolts, one nut, or something like that).

I removed the shifter cables. Squeezed the plastic retainers together to slide them out of the keepers then pry up to pop the ball and socket joint apart. Unbolted the bracket that held the cables (3 bolts) from the tranny (it was in my way later removing an engine to transaxle bolt). Removed an electrical plug connection from the front (radiator) side of the transaxle.

Disconnected the hydraulic line that runs from the slave cylinder in the tranny to the clutch master cylinder. The fittings disconnect by gently pulling the metal clip until it slides out partially. Then the tubes pull apart. I removed all the holders and clips, then used a zip tie to hold the shifter cables and the hydraulic line out of the way.

Then I loosened the lug nuts. Then I jacked it up and put it on jackstands. Removed the wheels. Drained the transmission fluid into a pan (8mm allen wrench for the drain plug, couldn't fit my 8mm hex socket in the space available).

Remove the nut and bolt holding each lower ball joint together (18mm). This time I did NOT disconnect the tie rod ends or the sway bar. I was able to push the lower control arm down as I pulled the hub assembly out and back to separate them. I had to use a long pipe on one side but the other side came off easy.

Removed the cotter pin from the end of the cv axle and removed the metal washer and keeper. This time I had a cordless impact gun to remove the cv axle nut (1 1/4 inch worked correctly on the nut; don't know the metric equivalent).

This time both CV axles came out the hub pretty easy. Once the outer end was free on each cv axle, I pried the inner end out of the tranny on each side. Be careful where you pry, of course.
At this point I removed the PTU. There were 6 14mm bolts holding it (5 are all in the same plane, one is significantly longer--this one was also very stuck this time. used some spray penetrant and impact to remove it). Three of the shorter bolts are easily removed from the bottom. One of the top two short bolts had to be taken out from the top. The second top bolt was easier to access from the passenger wheel well with a lot of extensions. The long bolt was also accessible from the passenger wheel well.

The PTU and transaxle separated easily this time. The large o-ring had a 1 cm tear on the bottom; the torn piece was still present but separated and flattened. I suppose I tore it during reassembly (last time I installed it on the transaxle and then mounted them both to the motor; this time I installed the transaxle and then mounted to PTU last.)

Next I loosened all of the transaxle to engine bolts.

The starter has two 15mm bolts holding it onto the bellhousing (at the top of transaxle towards the front/radiator side). There was also a 13mm bolt near the starter that was holding on part of the air assembly. There were two 14mm transaxle to engine bolts on the top as well.

There were a number of transaxle to engine mounting bolts accessible from underneath the car. 5 or 6 visible from under the front bumper. There is one that is very difficult to reach that I didn't re-install last time. By removing the PTU first, this bolt would be easier to access, but still pretty difficult so I left it out again (I did find the bolt in the garage--- yay for being a packrat and keeping everything). For those of you doing it the first time, remove the PTU first and then its much easier. Otherwise, the PTU is in the way. You have to use a 14mm shallow well socket with a pivot adapter and a short extension. With a small pipe over the 3/8 ratchet we were able to break it loose and then remove it using our fingers (very slowly). I left the rest installed at this point but broke loose. (One actually broke this time; I used never-seize when I put it all back together to try and prevent losing anymore if I have to remove the tranny again).

Next there were three drivetrain mounts, one in the back (between drivetrain and firewall), one at the front (between the drivetrain and front bumper) and one at the drivers side end of the tranny at the top of the drivers wheel well.

I put a jack under the engine oil pan (with a piece of plywood on it to prevent damage to the pan). The rear bracket bolt is hard to access (16mm); once again the easiest way is through the passenger wheel well. The nut is held onto the bracket by a "keeper nut" although it may fall off if bumped. The front mount bolt is easier to access, but the bolt is welded to the bracket, so it won't turn no matter how hard you try; so make sure you put the ratchet on the bolt! The bar going under the drivetrain is held on by 2 15mm at the front and a short 18mm at the rear. I removed the front mount bracket from the transaxle to give me more room later when removing it from under the car (2 18mm I think). The top mount bolt is easy to access. I also removed the top mount bracket (3 18mm bolts) to give me more clearance for removing transaxle from under vehicle.

With the plastic cover removed from the 'front' (facing engine) section of the transmission bellhousing, it was possible to see the modular clutch to flywheel bolts. They are an 18mm. I had to put a socket on the crankshaft bolt (22mm) to turn the engine so that I could find each of those 4 bolts. A breaker bar on the crank bolt allowed us to hold everything still while we broke these four bolts free and removed them.

Then I put my tranny jack under the transaxle and completely removed the transaxle to engine bolts. A gentle 'shove' and my transmission disconnected completely onto the jack, and I lowered it and pulled it out from under the car.

Last time, I removed transaxle to replace the slave cylinder, which was held on by two bolts (10mm). Had to disconnect it from the short pipe with the bleeder valve (that passes thru bellhousing) by pulling the metal clip partially out and pulling the pipes apart. Then bolted up new slave cylinder and popped hydraulic lines back together and pushed metal clip back in till it snapped in place. I went ahead and put in a new modular clutch as well (too much work to have to do again anytime soon; original clutch had 132,000 miles).

I replaced the Drivers side CV axle seal (0518 9989 AA) while the transaxle was out. I bought a seal removal tool (never had one before, it worked way! better than a screwdriver and was only $8 at Harbor Freight). Also bought a $16 seal install set and the new seal popped right in.

I didn't have so much luck with the passenger side seal (6800 5623 AA). On this 4wd the passenger side seal is in the PTU. I tried installing it while transaxle was still out, but couldn't get it in. Perhaps if I had waited until the PTU was mounted to the transaxle and everything was solid and not moving maybe it would have went in easier. I actually ended up just putting the old seal back in, because it would go (the new one just wouldn't fit). This seal wasn't really leaking to begin with (maybe a drip or two, but most of my leaks were orings and drivers side cv axle seal).

There are two o=rings between the PTU and transaxle. No one could find a part number for the small one, so I used the closest match I had in a Viton oring kit I had previously bought (also at harbor freight). I got a new large oring from the Jeep dealership (6800 5267 AA). I put a little Vaseline on each one to hold it in place and help everything slide together. I put them onto the PTU while the transaxle was out so I had room to work, then I sat the PTU aside and installed the transaxle.

I cleaned out the bellhousing. I lubricated all the bolts with never-seize and then ran the bolts into all the holes while the transaxle was still out and assessible. If I had had the right size tap and die, I would have gone over all the threads with that, but I didn't so cleaned everything up with a wire wheel. I rolled the transaxle back under the car, jacked it into position. It is difficult to the rear mount lined up right, but the transmission jack makes the job a lot better. I got the transaxle to engine bolts started and snug. Then I put the four flywheel to modular clutch bolts back in (had to turn the crank again).

The PTU lined up and slid together easy onto the transaxle this time. Got all the bolts started and snugged.

The rest of re-assembly was pretty much reverse of removal. Nothing special, just make sure to tighten all the bolts and use torque wrench when possible.

I bled the clutch hydraulics by opening the bleeder at the bellhousing while my helper kept the master cylinder reservoir topped off. The pedal still felt soft, so I closed everything and I pumped the pedal a bunch of times (50 to 100 times) and then bled it again. Got more air out. Let it sit overnight, and repeated. After the 3rd time, clutch feels decent. I'll probably try bleeding again after a week of driving to remove any more air that may be in the system. Filled the tranny with ATF+4, about 3 quarts give or take. I replaced the two rubber plugs with new ones (much more pliable than the old ones, and only 5 bucks each).

Spent about $100 bucks on seals this time (dealership parts prices; no parts store could find the right seals). But the labor was cheap!

Removal and installation took a total of less than 8 hours. Removed one evening and re-installed the next day. Removed by myself, but had help with raising the transaxle back up. It would be possible but REALLY hard to line up the engine and transaxle without an extra set of hands.

So I should have replaced the seals last time, but couldn't find the parts anywhere (even the dealership had to order them for me this time; they didn't have them on hand). And it was my fault the oring was damaged. But I learned a little something last time and that made it easier the second time. It was 28,000 miles and 18 months inbetween the two removals. Vehicle now has 169,000 miles on it.

The good news is the main leaks are gone! I was putting a half a quart of ATF-4 in a week (she drives a lot for work). Wouldn't be so bad if the tranny fill was easier to get to---BUT its a PITA, so glad I won't be doing that so much anymore.

Still have a small drip from the passenger side CV axle seal. I'm going to order another new seal and try again to install it with transaxle in place (maybe it will be easier without the PTU flopping around).

Once again, I hope someone finds this useful. I actually looked up my last post to remind myself before doing the job this time!
 

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great detail thank you! I have done this job 8-10 times with several patriots. i recently however replaced the Passengers side PTU Axle seal 3 times and still had a leak:rolleyes: So i had a good look at the axle that had just over 200,000miles on it and it had a very small amount of movement internally so i went to the auto recylers and pulled one from an automatic 4x4 compass and it had no play and solved my leak issue without replacing anymore seals. I certainly did not think that the axle would wear to the point of seal leakage but it did.
 

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Discussion Starter · #7 ·
So just wondering why it was necessary to pull the whole transmission to repair a seal between the PTU and the transmission? I have a leak between my CVT and the PTU, so I was thinking all I needed to do was pull the PTU and replace the seals?
I didn't actually know that the PTU o-rings were the cause of the leak. I couldn't really tell where the leaks were coming from. Also, I knew I could pull the tranny without major headaches since I had done it before. Removing the PTU would have been starting from scratch trying to figure out how. But I suppose I could have disconnected the PTU and removed it by itself if there was room. Dunno, never tried...
 

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Discussion Starter · #8 ·
The instructions for pulling the ptu say there are 6 bolts around the perimeter three on the bottom and three on the top. The center hole was empty on the top (on mine) did not find a long bolt maybe I missed one because I can't get it to separate.
There is a 7th bolt that is different than the rest. If I recall correctly it is much longer. It is lower down than the top 3 bolts. Also it is in a different plane (hence the different length). So while the top 3 and bottom 3 are relatively easy to go from one to the next (feeling your way along) this 7th one is in a totally different place. I used a bunch of different extensions and swivels to get it out, and due to the difficulty didn't put it back in after I removed the tranny the first time.
 

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The plastic retainer clips on my shifter cable are damaged badly. Unsqueezable. Does anyone have suggestions on how to get them out?

Edit: Nevermind. I used the smallest router bit I had for the dremel, and just gently ground out the plastic.
 

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great detail thank you! I have done this job 8-10 times with several patriots. i recently however replaced the Passengers side PTU Axle seal 3 times and still had a leak:rolleyes: So i had a good look at the axle that had just over 200,000miles on it and it had a very small amount of movement internally so i went to the auto recylers and pulled one from an automatic 4x4 compass and it had no play and solved my leak issue without replacing anymore seals. I certainly did not think that the axle would wear to the point of seal leakage but it did.
 

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So I had to pull my wife's transmission again (2007 Jeep Patriot 4x4 5 speed manual 2.4L). I pulled it about 18 months ago to change the slave cylinder. I posted some info then, and I'm just going to update now since I feel like I did a better job the second time around.


I pulled the transmission this time because it was leaking ATF fluid between the transaxle and PTU. There are two o-rings between the transaxle and PTU. I isolated all the leaks over the course of several days and when I was confident it was leaking at this location, I decided to pull the tranny again and replace the o-rings. The C/V axle seals were also leaking (although those can be changed without pulling the tranny).


Some of this is a repeat of my previous post, but I did things in a slightly different order this time with improved results.


First I disconnected and removed the battery. This required removing the airbox, etc. Airbox comes off by two twist knobs to remove air intake tube. Then I removed the large hose clamp from the airbox, unclamped the two sides, and removed them by pulling up and out. Then I removed the battery terminal connections and battery hold down bar (all 10mm). Next came the battery tray (which has four bolts and a nut holding it, 13mm).

Unbolted the computer so I can pull it up and out of the way. Removed the bracket that holds computer (2 bolts, one nut, or something like that).

I removed the shifter cables. Squeezed the plastic retainers together to slide them out of the keepers then pry up to pop the ball and socket joint apart. Unbolted the bracket that held the cables (3 bolts) from the tranny (it was in my way later removing an engine to transaxle bolt). Removed an electrical plug connection from the front (radiator) side of the transaxle.

Disconnected the hydraulic line that runs from the slave cylinder in the tranny to the clutch master cylinder. The fittings disconnect by gently pulling the metal clip until it slides out partially. Then the tubes pull apart. I removed all the holders and clips, then used a zip tie to hold the shifter cables and the hydraulic line out of the way.

Then I loosened the lug nuts. Then I jacked it up and put it on jackstands. Removed the wheels. Drained the transmission fluid into a pan (8mm allen wrench for the drain plug, couldn't fit my 8mm hex socket in the space available).

Remove the nut and bolt holding each lower ball joint together (18mm). This time I did NOT disconnect the tie rod ends or the sway bar. I was able to push the lower control arm down as I pulled the hub assembly out and back to separate them. I had to use a long pipe on one side but the other side came off easy.

Removed the cotter pin from the end of the cv axle and removed the metal washer and keeper. This time I had a cordless impact gun to remove the cv axle nut (1 1/4 inch worked correctly on the nut; don't know the metric equivalent).

This time both CV axles came out the hub pretty easy. Once the outer end was free on each cv axle, I pried the inner end out of the tranny on each side. Be careful where you pry, of course.
At this point I removed the PTU. There were 6 14mm bolts holding it (5 are all in the same plane, one is significantly longer--this one was also very stuck this time. used some spray penetrant and impact to remove it). Three of the shorter bolts are easily removed from the bottom. One of the top two short bolts had to be taken out from the top. The second top bolt was easier to access from the passenger wheel well with a lot of extensions. The long bolt was also accessible from the passenger wheel well.

The PTU and transaxle separated easily this time. The large o-ring had a 1 cm tear on the bottom; the torn piece was still present but separated and flattened. I suppose I tore it during reassembly (last time I installed it on the transaxle and then mounted them both to the motor; this time I installed the transaxle and then mounted to PTU last.)

Next I loosened all of the transaxle to engine bolts.

The starter has two 15mm bolts holding it onto the bellhousing (at the top of transaxle towards the front/radiator side). There was also a 13mm bolt near the starter that was holding on part of the air assembly. There were two 14mm transaxle to engine bolts on the top as well.

There were a number of transaxle to engine mounting bolts accessible from underneath the car. 5 or 6 visible from under the front bumper. There is one that is very difficult to reach that I didn't re-install last time. By removing the PTU first, this bolt would be easier to access, but still pretty difficult so I left it out again (I did find the bolt in the garage--- yay for being a packrat and keeping everything). For those of you doing it the first time, remove the PTU first and then its much easier. Otherwise, the PTU is in the way. You have to use a 14mm shallow well socket with a pivot adapter and a short extension. With a small pipe over the 3/8 ratchet we were able to break it loose and then remove it using our fingers (very slowly). I left the rest installed at this point but broke loose. (One actually broke this time; I used never-seize when I put it all back together to try and prevent losing anymore if I have to remove the tranny again).

Next there were three drivetrain mounts, one in the back (between drivetrain and firewall), one at the front (between the drivetrain and front bumper) and one at the drivers side end of the tranny at the top of the drivers wheel well.

I put a jack under the engine oil pan (with a piece of plywood on it to prevent damage to the pan). The rear bracket bolt is hard to access (16mm); once again the easiest way is through the passenger wheel well. The nut is held onto the bracket by a "keeper nut" although it may fall off if bumped. The front mount bolt is easier to access, but the bolt is welded to the bracket, so it won't turn no matter how hard you try; so make sure you put the ratchet on the bolt! The bar going under the drivetrain is held on by 2 15mm at the front and a short 18mm at the rear. I removed the front mount bracket from the transaxle to give me more room later when removing it from under the car (2 18mm I think). The top mount bolt is easy to access. I also removed the top mount bracket (3 18mm bolts) to give me more clearance for removing transaxle from under vehicle.

With the plastic cover removed from the 'front' (facing engine) section of the transmission bellhousing, it was possible to see the modular clutch to flywheel bolts. They are an 18mm. I had to put a socket on the crankshaft bolt (22mm) to turn the engine so that I could find each of those 4 bolts. A breaker bar on the crank bolt allowed us to hold everything still while we broke these four bolts free and removed them.

Then I put my tranny jack under the transaxle and completely removed the transaxle to engine bolts. A gentle 'shove' and my transmission disconnected completely onto the jack, and I lowered it and pulled it out from under the car.

Last time, I removed transaxle to replace the slave cylinder, which was held on by two bolts (10mm). Had to disconnect it from the short pipe with the bleeder valve (that passes thru bellhousing) by pulling the metal clip partially out and pulling the pipes apart. Then bolted up new slave cylinder and popped hydraulic lines back together and pushed metal clip back in till it snapped in place. I went ahead and put in a new modular clutch as well (too much work to have to do again anytime soon; original clutch had 132,000 miles).

I replaced the Drivers side CV axle seal (0518 9989 AA) while the transaxle was out. I bought a seal removal tool (never had one before, it worked way! better than a screwdriver and was only $8 at Harbor Freight). Also bought a $16 seal install set and the new seal popped right in.

I didn't have so much luck with the passenger side seal (6800 5623 AA). On this 4wd the passenger side seal is in the PTU. I tried installing it while transaxle was still out, but couldn't get it in. Perhaps if I had waited until the PTU was mounted to the transaxle and everything was solid and not moving maybe it would have went in easier. I actually ended up just putting the old seal back in, because it would go (the new one just wouldn't fit). This seal wasn't really leaking to begin with (maybe a drip or two, but most of my leaks were orings and drivers side cv axle seal).

There are two o=rings between the PTU and transaxle. No one could find a part number for the small one, so I used the closest match I had in a Viton oring kit I had previously bought (also at harbor freight). I got a new large oring from the Jeep dealership (6800 5267 AA). I put a little Vaseline on each one to hold it in place and help everything slide together. I put them onto the PTU while the transaxle was out so I had room to work, then I sat the PTU aside and installed the transaxle.

I cleaned out the bellhousing. I lubricated all the bolts with never-seize and then ran the bolts into all the holes while the transaxle was still out and assessible. If I had had the right size tap and die, I would have gone over all the threads with that, but I didn't so cleaned everything up with a wire wheel. I rolled the transaxle back under the car, jacked it into position. It is difficult to the rear mount lined up right, but the transmission jack makes the job a lot better. I got the transaxle to engine bolts started and snug. Then I put the four flywheel to modular clutch bolts back in (had to turn the crank again).

The PTU lined up and slid together easy onto the transaxle this time. Got all the bolts started and snugged.

The rest of re-assembly was pretty much reverse of removal. Nothing special, just make sure to tighten all the bolts and use torque wrench when possible.

I bled the clutch hydraulics by opening the bleeder at the bellhousing while my helper kept the master cylinder reservoir topped off. The pedal still felt soft, so I closed everything and I pumped the pedal a bunch of times (50 to 100 times) and then bled it again. Got more air out. Let it sit overnight, and repeated. After the 3rd time, clutch feels decent. I'll probably try bleeding again after a week of driving to remove any more air that may be in the system. Filled the tranny with ATF+4, about 3 quarts give or take. I replaced the two rubber plugs with new ones (much more pliable than the old ones, and only 5 bucks each).

Spent about $100 bucks on seals this time (dealership parts prices; no parts store could find the right seals). But the labor was cheap!

Removal and installation took a total of less than 8 hours. Removed one evening and re-installed the next day. Removed by myself, but had help with raising the transaxle back up. It would be possible but REALLY hard to line up the engine and transaxle without an extra set of hands.

So I should have replaced the seals last time, but couldn't find the parts anywhere (even the dealership had to order them for me this time; they didn't have them on hand). And it was my fault the oring was damaged. But I learned a little something last time and that made it easier the second time. It was 28,000 miles and 18 months inbetween the two removals. Vehicle now has 169,000 miles on it.

The good news is the main leaks are gone! I was putting a half a quart of ATF-4 in a week (she drives a lot for work). Wouldn't be so bad if the tranny fill was easier to get to---BUT its a PITA, so glad I won't be doing that so much anymore.

Still have a small drip from the passenger side CV axle seal. I'm going to order another new seal and try again to install it with transaxle in place (maybe it will be easier without the PTU flopping around).

Once again, I hope someone finds this useful. I actually looked up my last post to remind myself before doing the job this time!
Thank you
this helped a lot.. easy way to do a clutch and slave replacement drop the entire motor and transmission remove the k frame takes a little more work but if you are doing this yourself with a car lift jack up the rig both sides up about 24-36 inches use your tires and rims for blocking. drop the k frame un bolt the sway bar and steering rack your mounts next just loosen the bolts. preferably you have rope or chain you need to have a tree that is sturdy or a good roof rafter to hold up the engine and transmission up with when its unbolted.. just throw over a strong rope or chain.. works well.. find the hang point to balance the unit ... then use two jacks to drop the motor remember to disconnect your drive shaft at the tail end of the transmission. ikts 4 bolts 13 mm heat them up with a propane or butane torch if need be. easy to take tranny apart.. and remember that hidden bolt up behind the transfer case its 13mm get all the bolts out and pry apart. fix it put it together lift unit up into place ad put back together as common sense would be.
 

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I tried the pry bar/brute force to get the CV axles out of the transaxle and couldn't pry them out after a lot of swearing. On the passenger side, I used a small bar as a punch and tapped it with a hammer against the CV axle at the transaxle and it popped out easily. Used a pry bar on the driver's side and tapped the pry bar a hammer and out popped the half shaft.
 

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The instructions for pulling the ptu say there are 6 bolts around the perimeter three on the bottom and three on the top. The center hole was empty on the top (on mine) did not find a long bolt maybe I missed one because I can't get it to separate.
Old reply: There is a top center hole but the center top bolt is lower down than the other two and under the manifold. You can access it using a 3 foot long extension from the passenger side wheel well.
Make sure that you clean out the channel on the opposite side of the bolt head because there's a bolt hole on the drivers side that you can't see. The channel fills with dirt and water and rusts the screw tip end of the bolt which freezes the bolt in place (galls) and then you are screwed like me. Fill the channel with penetrating oil and let it sit for 12 hours.

In my case, I have 5 out of 6 bolts removed and the most inaccessible bolt (the top center) is frozen and the head is stripped after 4 hours of trying to get it out using every method I could think of. I could only unscrew the bolt about 1/4" - I tried slowly turning it in then out, tried exercising the bolt using an impact gun and after 4 futile hours over 2 days, the bolt head stripped. You need to remove the PTU to take out the rear transaxle mounting bolt.

Expect that one or two of the bolts removed somewhere in the process will gall and strip the aluminum threads. I had one of the top left transaxle mount bolts gall and strip. Looks like they didn't put any anti-seize on the threads so it will be heli-coil time.
 
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