Electronically, the only difference on the engine proper is the TPS - and you don't even have to swap that until it fails later (you use the three-pole plug for the manual, and the four-pole plug can be ignored or just left put.)
The transmission controller is on the backside of the bottom dash trim under the glove box & cargo area, so you can disconnect that. You'll also have to bypass the NSS connection (can't remember which terminals to jump offhand, but it can be looked up fairly quickly if you've an FSM...) so you can start the thing, but you'll be fine otherwise.
Take the clutch and brake pedal from the donor rig - you'll need to swap the brake pedal as well.
The shifter stuff should be fairly obvious. I think there's a blanking plate in the transmission tunnel that closes off where the shifter for a manual would go - if it's rivetted in, just drill out the rivets. A small bit - ~1/8", I think - should serve.
If you're putting in an AX-15, you'll need to bear in mind two things:
1) You've probably got your crossmember in the front set of framerail holes. You'll use the rear for the AX-15 - if those holes are stripped out (they have threaded inserts, but they can rust away...) you'll need to cut "access ports" in the framerail so you can use nuts and washers on the bolts.
2) Depending on when your 1989 body was made, you may have to extend the hole in the transmission tunnel to the rear of the body. Early unibodies would have been set up for the Peugeot that year, which has the shift tower farther forward. As I recall, you need to extend the shift tower hole about two inches toward the rear of the vehicle - takes a few seconds with an angle grinder.
Even though you're not swapping "Peugeot to AX-15," you may find information in this thread useful -
http://www.naxja.org/forum/showthread.php?t=70388. Read it over, and you'll get some more ideas to check into before you dig into the swap, I think.
