Having used a similar donor motor from a 2004 Mach 1 here is what I did. I had Art Cuesta do a wire diet on the OEM harness. As part of the wire diet, we eliminated the secondary O2 sensors, EGR, reset the fan temperature threshold, eliminated the PATS, and added a performance tune. The reprogramming is achieved by adding a Diablo sport piggy back chip programmed by the tuner he uses. If you have some room in your budget for the wire diet, I highly recommend it. Having Art do the wire diet is one of the best ways to assure your engine starts the first try. If you do not flash out the PATS, you need to keep the gauge cluster and the key module from the steering column. With PATS, if these items are not present and matched to the ECU, you will get a no start. Good luck, it is a big motor, but it fits, just barely.
Alan