You can use any 4R70W with a 2 bolt starter, that is the easy way to differentiate the two bell housing bolt patterns. The 4.6/5.4 engines have different pattern, including the 3 bolt starter.
The 98+ models have a better mechanical diode intermediate clutch, and very slightly improved VB's, and electrical parts. None of that is critical for a stock build, so don't worry too much about that. The differences affect you just for the parts I mentioned before, to make the 98+ models work for you.
Your output shaft will surely be okay, so feel free to get a 4WD or AWD trans if you have to. The 5.0/3.8/4.2 should all be the same 2 bolt trans case, and almost all internal parts are the same from 98 up. That gives you a lot to choose from.
Have them replace all of the electrical solenoids, they don't cost much. Remember that you need to use a TCC solenoid made for your 96 model, that's the torque converter clutch solenoid. You also have to use your range sensor(DTRS/MLPS), as it has fewer wires. The electronic signals changed in 98+ model PCM's, thus you have to use the correct TCC and DTRS.