By time you reconfigure the 1999-2004 V6 to work well with the 1996-1998 electronics you will end up with almost the same motor (3.9 vs 3.8). But with the same intake so no real improvement in air flow.
At the end of the day the swap gets you a newer motor that's internally balanced that's very close to the original motor after a fair amount of work.
If the original motor is tired and in need of help it maybe wiser to rebuild the motor that you have.