My truck was converted from auto to manual, I actually believe that a cable just runs from the shifter to the tranny, But IDK, I didn't do the swap in mine. My mom has a Mail Jeep DJ-5G with a Torqueflite 904, which I believe the 86 used, and it just uses a cable, no electronics. All of the shift points are set on the tranny.

Actually I did the exact same thing you are about to do, in my 87 2wd Manual, I took the carb out and the whole vacuum system out, I have about 5 wires on the passenger side, rather than the 15 or so that came out of the computer