Over the years, the general consensus seems to have been "sell what you have and buy what you want".
The reason behind it is this, finding all the pieces you need is easiest done by buying a donor, and if that's what you're going to do, then you keep the donor and get rid of the one you no longer need - they are going to be times when it makes sense to swap, but more often than not, it won't - if you can get a donor cheap (say with a blown engine or front end damage), then by all means go ahead.
What do you need ...
ECU & wiring harness (the 4 speed is electronically shifted and the TCU is usually integrated into the ECU), the transmission and I believe the cross member, the front & rear drive shafts, the front & rear diffs, all the interior bits, shifters. console bits, pedal box.
The 3 speed might be easier, depending on which engine you have in your second gen, but, you're most likely going to be looking at some degree of custom fab, crossmember, drive shafts, and you'll need to figure out axle gears and a vacuum modulator (this is what controls the transmission shift points) and where to connect it.
