If both transmissions are W56, then it really won't make any difference which transmission you use. If you don't know the history of either, pull the drain plugs and use the one with the best looking oil and a clean plug.
Like others have told you, the crossmember will need to be moved back and the shift holes on the floor will need to be moved back. Some guys use "U" bolts over the frame to bolt up the crossmember. I fabed up new ends for my crossmemebr and made threaded bosses that I welded to the frame. There are also some adjustable plates to make your stock crossmember work. I know Northwest Off-Road has them in their catalog, but I have never seen one. I tend to stay away from adapters and universal stuff like that if I can. Drivelines are pretty much a custom deal.
Can you get more parts off the 93? If so, you may want the steering box. rear axle housing, front brake calipers (front hubs are an option too). The brake calipers from a V-6 truck are really more desireable, but the 4 cylinder ones will get you to the vented rotors. There is a ton of stuff you may want to think about. Spend some time reading and searching and you will get lots of good information about upgrades.
Are you going to stay with the 20R?
