Woy, yes, the ECU is different for the auto vs. manual. Different part numbers. Also the auto wiring harness has several additional connectors that hook up to the tranny that are missing from the manual harness.
Yes, the exhaust on the 2000 2.5L is a bit undersized for the 2.7L. There is also quite a restriction on one side. The engine would breathe a lot better if fitted w/ a late model exhaust. It would be nice if the aftermarket would come out w/ a performance exhaust system that included the downpipes, and perhaps even a set of headers.