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I think you'd have a tough time with that exchange. The upgraded engine and 5 spd tranny of the 2002-2004 might be made to physically fit where the original engine and 4 spd sat in the 1999-2001, but getting the ECU/TCU to work? Even if you also moved the computers, are all sensors and connectors identical? I doubt you'd ever get it to run right, and code free.

There is a shop manual available on CD (and maybe still as a download) that has years '99-'03 all together. You might be able to examine in detail the electrical diagrams of the two different series and see if everything would line up. Same with engine & tranny mounts, half shaft lengths & part numbers, etc.
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