I'm kind of in line with JamesR.
I set the clutch in position and tightened the pressure plate just enough to hold the disc in place. Without the bellhousing on, and although it was heavy and cumbersome, I was able to take the assembled transmission (disconnected from the transfer case and cross member), slide it into the clutch splines and guide bearing, then tightened the pressure plate bolts a little at a time, crossing back and forth until they were all tight.
Note: The transmission shaft was wired in place so the shaft would stay in position. Also, my Willys is completely disassembled for a restoration. It made good sense for me to do it this way. (I didn't take the transmission totally apart as the prior owner had done this a few years ago.)
Note: The transmission is a bit heavy assembled. I had it sitting on some blocks while I used it to align the clutch. This also assured that the splines on the shaft and the clutch mated and were the right size.
I know this is goofy, but it worked for me.
Tim