If the v6 in the entire range of 4th gens is the same, any idea why car-part.com shows only 03-04 when you search for 04 and when you search 06 it shows 05-09? I'd opt for the later years because of the real or perceived head gasket fix.
Probably because its a different transmission that its bolting to. This relationship probably had an effect on the ECU as well.