Well luckly for you the 2.8L, 2.9L and 4.0L are all in the same family of engines. The bolt pattern for the bell housings are the same. Depending on what you are going to do you I would either recommend a TK5 for a stock truck or the 4.0L's M5OD. Actually get the M5OD. it can be had from early explorers and pretty much any ranger based vehicle with the 4.0L.
Although the TK5 will be less work because you don't have to move the crossmember around.
For the T case I would say the BW 1350 should be fine and it will come with the TK5, the 1354 was on later models and is harder to find in a manual setup. But get a manual it will be worth it.
OK so if you go with the TK5 you just need to find a donor truck with the parts would be the easiest. I don't know what all you will need but I do know you will need the clutch pedal assembly, slave and master cylinders, the hydrolic lines, Flywheel from the vehicle with the same transmission, also clutch and pressure plate for that flywheel, and starter for that trans and flywheel so it matches up. There maybe other stuff associated with it too but I have only owned sticks and haven't fooled around with them too much.