Software and desoldering the chip from the board?
Take a look at this site: www.carmodder.com ? EEPROM Programming for Beginners for the Holden VZ Commodore
A $100 EEProm programmer and a chip clip is all you should need. I expect the VIN will be in plain text and you can change it out if needed. For my Caprice, I read the vin off a junkyard radio and will be changing it before putting it in. Was not that hard (I'm also a total noob to this). I haven't looked into any Chrysler products, but it should be similar.
I'm sure the dealership could also program the new vin in, but sometimes they are reluctant to do something that isn't a straight swap. If all else fails, contact Welcome to White Auto and Media Services , he might be able to help, he does a lot in the G8/GM world, but charges a bit for it, not sure if he has done anything with Chrysler products.
Now the other 1/2 would be to check to see if the the Body Control Module programing is any different for cars with the EVIC models or not. The Wrangler guy saying it was plug and play seems promising.