Yes, the 2.9 bell housing pattern never changed, so they will all bolt up.
Some had no EGR system so if you get an engine without EGR plumbing, try to get the PCM for that engine too. It'll be a pain to add egr plumbing to a non-EGR engine, but it's easy to block off EGR if your replacement engine has it and you don't need it for your original setup (so you can use your original PCM). You also need to pay attention to the crankshaft pilot bearing, I believe the auto and manual differ.
Obligatory opinion.....for the amount of work you are facing, swap in an early 4.0 instead. Bolts right up but there will be some electrical work, 4.0 harness/PCM, starter, etc.