About ten tears ago I had a 2000 S with a 1997 2.5L engine in it.
The engine wire harness from the 1998 engine will not plug into the 2000 S ECU. You can use a throttle body and wire harness from a 2000 - 2002 engine on your 2.5L if you adapt the intake to make it fit.
If you can post some pics of the wires at the ECU and a view of the engine with the cover removed, I can probably help to sort thing out.