Jay, a good guy to contact is Art at Wirediet.com because he REALLY knows the 4.6 wiring. Here's a link to a recent thread that may be useful:
http://www.ffcars.com/forums/45-ford...-6-wiring.html

I used a 2000 Mustang GT donor and used the OE engine harness which I had "dieted" and the OE computer flashed. I used the ISquared (now ISIS) harnesses for the chassis and dash wiring, but things have improved in the last 3 years. Art is the best source, I think. BTW, you'll love the 4.6 engine.
Pete