I lost keys to my 2002 mustang v6 so I went to salvage yard and pickup lock cylinder with key and Ecu from a mustang that was the same year and same engine and it still won’t start I program the keyfobe the doors unlock and lock trunk opens from remote any one know what’s going on Thanks .
The cluster and PCM are programmed to each other. Changing either one or the other will invalidate PATS. Just as with loosing the keys.
My recommendation. Put the original PCM back in because it's the one that matches your car's VIN. The look over this information about a possible DIY option to reprogram new PATS keys.