I'm in the process of doing this all right now. I had a 91 4wd that I rolled. Then I got an 89 2wd for $200 and got it running. I've already bolted the front axle in with NO modifications needed.
The shifter hole for the 4wd is already cut into the floor and has a metal plate bolted over it. there is a pivot bracket that also bolts to the floor around the drivers side of the "hump" just a little down and forward of the shifter hole. The indention for the bracket is already in the hump, and there are 4 little dents that show you where to drill the holes. Its literally screaming to be 4wd.
The only thing to remember is to get a tranny/transfer case with the same type of speedometer sensor (either cable driven or electric). I am doing a super shorty SYE at the same time, so I will be converting to electric from cable, but haven't done it yet. I am working on a write up for swapping a 91-97 guage cluster (w/ electric speedo) into the older one with cable speedos.
I am also having to swap the crankshaft position sensor from the 2wd tranny over to the 4wd tranny because the 89 is 2 wire and the 91 is 3 wire. Other than that, just make sure (obviously) that the front axle has the same gear ratio as the rear already in the jeep!
But as long as the donor stuff is from the same year or mini generation (84-86?, 87-90, 91-97) everything should bolt in (other than the pivot bracket holes you drill out)