I have 2 2003 Mustang GT’s. One of which was crashed previously avoiding a heading on collision with a drunk driver, the other I picked up with a blown motor but mint condition body. In order to make it easy to identify which mustang I am talking about here I’ll identify them as:
Mustang A (crashed one with a good motor, bad body, manual transmission)
Mustang B (Bad motor, good body, Automatic Transmission)

So recently I swapped over the engine and trans from Mustang A into Mustang B.
Mustang B was originally an Automatic
After the swap I found my myself with a theft light blinking and a crank no start, I am aware that the crank no start is from the theft light (PATS system)

I have tried everything from swapping their ECU, Keys and key cylinder, cluster gauge, CRRM. But nothing seems to work and I still have this theft light and my mustang is taken apart into pieces. The only thing left to swap over from Mustang A to B is the clutch pedal.

Any ideas on what could be the cause of this and any possible remedies?
 
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You need to use the PCM that also MATCHES the transmission used. There is a difference between an automatic/manual PCM.

The ignition lock cylinder itself will not affect PATS (the chip will). My recommendation is to use the one that the key cut matches the door.

This thread does not state IF either PCM will "talk" to an ODB2 scanner or IF the mileage displays upon the cluster during initial key on. Why is this important? Because it indicates if the PCM is alive and able to communicate with the cluster.

Here's some more information that may be of help.

1996+ Crank with no start check list

If we assume that at one point in time that the PCM, Cluster, and keys all matched, then it will be necessary to trouble shoot a possible power or communication problem. Regardless it's important to perform the trouble shooting steps in a logical manner going where the test results take you. This will avoid wasting trouble shooting effort or attempting to "part swap" into a fix.

Assuming the only thing wrong is the need to re-program PATS, here's some information on a possible DIY solution for PATS reprogramming. I strongly recommend for you to consider getting an ODB2 scanner as it may prove vital in this and other trouble shooting.

ForScan ODB2 scanner w ELM327 USB
 
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