Engine Swap - transmission needs

[Aanic]

I've just about decided to either rebuild or replace my 99's 2.5l motor. If I replace, I'm looking at a potential upgrade. Big question is, will the 5 speed from the 2.5l fit any of the options?

2.5l - direct replacement, no issues
2.7l - 00-02 swap
3.2l - 00-02 swap
3.4l - 996 engine

I'm warming up to the idea of spending the next year buying and prepping an engine, then doing the swap when this one cuts loose. Need to factor in the transmission needs into the budget.