With the exception of EGR I', pretty sure that 01-03 are the same. 04 is when they did a big change to the electronics. 04 and up manual trasnmissions have a taller final gear ratio that brings the rpm down but not sure if the pcm can work with that. As far as pcm, you do not need to replace the pcm with the motor. AS for the rest of everything it should be a straight across swap. If your engine has an EGR then make sure the replacement has one also. That's about all I can think of that would be a deal stopper.
