I would say you will need the flywheel and ECM from the same year XJ or MJ.If you keep these the same year (90) as your present XJ, then the rest of your electronics (distributor, etc.) should work. I have heard of people using the automatic wiring harness with a manual tranny. Somehow they take out the auto tranny's computer. I have no experience with that though. If no one chimes in, I'll search around and see who has done this. In my case, I went with a '95 manual wiring harness, ECM etc. I swapped in an '03 block and a '95 head. I could have still used the '88 Renix wiring though. Some prefer the Renix system.
Tom