Here's the deal in a nutshell. The YJ came out in 87. The standard transmissions in YJs up to about 90-91 are crap. Then, when the tranny got better, they went with this internal (inside the bellhousing) hydrauilic slave cylinder / hydraulic throwout bearing thing which is really hard to replace. That went external to the bellhousing in like 92-93 or something (I'm not real sure on that one) At the same time, about 90-91, the terrible Carter BBD computer controlled carburetor system from the old 258, which YJs had up to then, was replaced with a new motor, the 4.0, and fuel injection. The transfer case is different from the old CJs too. The way the rear driveshaft is connected to the transfer case is VIA a slip yoke, which is not so great. If you take out the rear driveshaft, all the fluid comes out. This is not a large concern until you get into off-road situations where you break the rear driveshaft, and can't take it out and drive on the front shaft. There are kits available to upgrade the transfer case, it's what's called a Slip Yoke Eliminator, or a SYE.
The automatic transmissions in YJs have always been the 999, except I think for 87 and some of 88 which used a 904 or whatever. The 999 is a good tranny. All the transfer cases are a NP 231, again, except for 87, which had a NP 207 I think. Similar, but a little different. The NP 231 is a good transfer case, except for the slip yoke design, as I mentioned. The NP 231 is also a chain-driven case, as opposed to the Dana300 typically used in the older CJs, which was a gear driven unit.
Older is sometimes better to work on, as it's simpler, but it can also be real hard to get some of it apart, as bolts and stuff can be pretty hard to get out, as opposed to a 4 or 5 year old YJ.
OK, so it wasn't a small nutshell /wwwthreads_images/icons/smile.gif, but that's the story as best I know it.
Good luck with your hunt.
88YJ, 4"susp, 33"BFGMT, 9k#winch, rear homemade swingout, reb.258, 999, 4.10, weber32/36, GMHEI.