I just went through this not too terribly long ago with mine. I pulled the motor without the transmission, then used the cherry picker to drop the transmission/transfer case straight down onto a creeper (cherry picker stuck into the jeep and strapped to the transmission through the hole in the trans tunnel. When I put the motor back in I assembled it all together and dropped it in as one piece. It took a little pushing and shoving but everything went in pretty well.
These are the only pics I have, but I'm bolting the bellhousing back to the motor and the torque converter up so it can be dropped in. I would note that the load balancer that I have hooked to the engine was almost useless with the trans and transfer case hanging off of the back of the motor. I ended up using the tow strap (repositioned) to hold everything as I dropped it in.
If I had to do it again, I probably wouldnt change a thing. Everything came out and went back in pretty well. Dropping the trans and transfer case out without the motor in is pretty easy whether you use a tranny jack or the cherry picker like i did.
1990 YJ Islander, 4.2L MC2100 DUI HEI, 2.5" RE lift, 31x10.50 DuraTracs, HandenFab rear bumper / swing-out, Tough Terrain
off-road camp trailer.
Build thread: http://www.jeepforum.com/forum/f22/tys-yj-build-1502554/