Smart @$$ comment Terry - Both the manual and autos are 5 speeds.
If I am reading correct you want to put the 2.3/manual into '99/'00 which has 2.5/auto.
Assuming so, it is going to be bit of PIA. (I deal more with 3.slos/4.0s, so might make a couple mistakes here). That said, anything is possible.
'97 used return fuel line; '98+ uses single line. I also believe there are difference in ignition (dual plugs versus single). And of course, the manual versus automatic.
The easiest way is to find (get) a '99/'00 manual computer; then you can leave the 2.5 intact, just swap transmissions (and associated pedals, flexplate for clutch, wiring, etc) What I don't know is if '99-'00 2.5s have PATS (they aren't supposed to, but I don't like assuming.

)
Swapping the pedals/clutch master cylinder, flexplate for flywheel is just a bunch of wrenching. But then you hit the 1st snag - clutch pedal switch, hopefully harness has it.
Those are quick things I can think of.