a couple of people around here have done it, and their posts helped a lot. Even then i still made a bunch of mistakes along the way...i thought i bought door wiring from a '96XJ from a member on here that isn't around anymore. Turns out everything was from an '89XJ (totally different connectors) and one of the regulators wasn't good. Lessons learned: get an FSM before tacking big projects and use as much wiring from the same year as your MJ as you can. I also carried a small project battery to the jy so i could test the window regulators before i pulled them. Also helped to be able to move up and down while pulling the wiring and regulators. And i've been lucky so far, the only electrical gremlin to pop up was a bad alarm the PO installed, it would go off randomly and drain the battery.
Do you still have the 89 wiring harness? I am in need of a pre 91 harness (I think thats when the connectors changed) I have a post 91 harness I would be willing to trade. Just for clarification I need the harness that goes from door to door.