[Brian in Tucson]

I've never done the swap you're contemplating. If it were my car, if the 2.5 is running well, I probably wouldn't mess with it.

Some problems I see, you will have to use the automatic trans wiring. It's different from the manual, I believe. Your engine wiring will have to be transferred over.

Your 98 is mechanical throttle cable, the 01 is drive by wire so you may need to adapt the intake to use the older throttle body.

Will the trans bolt up? Don't know & don't know if you can transfer your flexplate over, either.

I'm in the process of putting an 00 to 02 2.7 into my 01 Boxster base with a 2.7. I know I'm gonna have to transfer the wiring over, and maybe the fuel rails. I guess I could have tracked down a 3.4, but it's all so complicated and I'm not an expert.

It seems to me, you're asking the wrong people. I would take a list of your questions and go see what your mechanic says. Your questions are valid concerns.