I would appreciate an explanation of there not being a marriage between PCM and a specific motor.
The exact same "long block" 4.6 is found in a number of different Ford "applications". This is further evidenced by the large number of people that have taken a motor from Crown Vic's and put them (with some external modifications) into Mustangs.
I'm sure it's easy to see that the PCM in a Crown Vic is different from a Mustang. And different from a F150. As long as the motor is "trimmed" as the PCM is expecting the PCM will not know the difference. Note, by "trim" this means the entire motor package including electrical and car body support systems.
So you see that "technically" there is a long list of PCM model years from multiple "applications" that could work in a transplant situation. Your challenge is going to be to figure out which will make the most sense to adapt to your intended use.
Since your 1996 4.6 is:
- non-PI
- coil pack
- return fuel system
- Car style intake
If your intention is to re-use the 1996 Mustang GT wiring harness then this will restrict the PCM to a 1996-1997 Mustang GT. 1998 has a strange two speed fuel pump. 1999+ uses COP ignition. So that's out.
Consider going to car-part.com and search for a PCM from a 1996 Mustang GT with an automatic. Use the calibration that comes with the PCM.
If using a stock PCM instead of an aftermarket PCM it seems to me the challenge is going to be the sum total of the wiring needed to allow the PCM to do it's job. Remember the PCM is going to be looking for things like an EVAP purge system and EGR. ABS/traction control. Anti-theft.
Systems in the car not really associated with the Motor. Perhaps a lot of "modification" in your future. Some of these issues are why some will choose a stand along after market PCM for such a transplant project.