It would sure be helpful to my understanding if there was confirmation that the PCM is alive and talking. This could save time by not chasing "wild geese".
With the key on, do not crank. Attach an ODB2 reader or scanner and attempt to access the DTC codes.
IF the PCM does not talk to the ODB2 reader, this confirms you are dealing with a PCM problem (not PATS per se). After a motor swap, the most likely cause for a apparently dead PCM is a blown fuse or missing connector.
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.