THat's some tough swaps. The '87 5speed should be the Peugeot BA10/5, they didn't introduce the AX15 until mid-year '89. You'll then have to figure out a way to mate your
transfer case to the 2wd Peugeot tranny, not really worth the headache for a light-weight tranny with a bad rep.
You would need to swap the entire wiring harness and computer between the jeeps, along with the drivetrain.
I wouldn't ruin a good Comanche like that, the 2.5L will be useless with what's probably 3.07 gears in the MJ's axles.
For good MJ info, including swaps, check out
www.comancheclub.com/forums .