My 5MT FDI has the stock 16 inch wheel and tires. I am switching to 215/70R16 Yokohama Geolander AT-S tires, same width and height as the FDII tires. They are .7 inch taller than the stock tires, so give me .35 inch lift. I am researching the pre-2011 and 2011 FDII springs, front struts, and rear shocks. I expect them to give me at least another .7 inch of ground clearance over the tires, if not an inch more ground clearance.
Since I don't have the extra weight of the skid plates and tow hooks, I may have slightly more ground clearance than an FDII. If I wanted more of the FDII stuff, I could add the skid plates and front tow hooks. My Mopar rear tow bar assembly gives me the equivalent of a rear tow hook.
Going beyond that into the FDII transmission stuff will get into powertrain computer control issues which go way beyond the difficulty and cost of the bolt on stuff listed above. Plus, I like the fuel economy and 5MT. Although, if I were to do it again, I might go for the FDI CVT, since it gives a selection of more transmission "gears" (really identifiable, controllable sprocket "ratios").