Let's see if we can clear some things up for you.
Yes you will need to reuse the original wiring harness. As far as the PCM is concerned the new motor needs to "appear" the same as the old motor electrically.
In the same vein the 1998 and older does use a different cam sensor than the 1999+. So because the motor needs to look the same (electrically) then the same style cam sensor (2 wire vs 3 wire) needs to be used.
The other difference is that after 2000.5 Ford switched to internally balanced V6's. Before that they were externally balanced. It's important to NOT switch balance parts between the different motor types.
Regarding the fuel system. A 1998 and older Mustang uses a return based fuel system. Where as a 1999+ uses a return-less system with a Fuel pump driver module (FPDM) to control the fuel pump. Since we need the motor to appear the same to the PCM that means the original fuel delivery method will need to be re-used.[/QUOTE
Ok, makes sense. So if I am thinking this through correctly, I will need to change the intake? The intake and everything above it is completely different, no fuel rails on the 01..... and what about the trans? The 01 came with the trans still bolted in place. I haven't checked to see if 97 harness will match 01 trans. Both the 01 and 97 trans are good, both automatic .