Here is what I did, I bought a new engine harness from the folks at Mass Flo.
http://www.mass-floefi.com/EFIwiring.html
I didn't want to take a chance on a bad wire causing a major failure with my supercharged engine, besides I broke about 90% of the connectors on the old harness. If you get this harness you will have to unwrap part of the harness to change which side the coolant temp sensor and the Air temp sensor is on. On the Mass-flo Harness the Air temp is on the passenger side and the Coolant temp sensor (for the computer not the gage) is on the driver side, the EFI Mustang intake the are opposite. I didn't catch this until I had was ready to plug it in, I was able to pull the wires back and change sides with the harness and the engine w/o upper intake in the car.