I dont think there would be much re-pinning involved if you were going from a 96 Tbird to a 96 Mustang .. what I would do is get an EVTM for both vehicles and compare the PCM pinouts to determine which if any wires are different. The Tbird will of course have wiring to the transmission and the Mustang being a 5 speed would not have the electronic controls - just inputs from the speed sensor and likewise .. these parts would need to be re-pinned or spliced into the existing transmisison wiring harness, along with a couple other small things like the clutch pedal position switch so your car wont start without the clutch being engaged. Other than that, it should be pretty straight forward both cars being 3.8 V6 engines the calibration should be about the same. If youre going for a different year, there could be other issues to deal with.
Re-calibrating your PCM would cost a little more but you could get a better tune while youre at it. The parts that are going to end up costing the most is all of the stuff required for a 5 speed conversion.