Under the hood, look at the coil on plug (COP) units. Each COP has a RED power wire. This is the +12 volt power source for the ignition.
IF F2.2, F2.8, and the ignition RED wire all have +12 volts at key on, THEN the CCRM is supplying power to the PCM.
IF there is key on +12 volts at the trunk mounted IFS switch, then the CCRM is good.
If this were my car, I would pull the PCM and inspect the printed circuit board for burned marks. A new PCM is likely in your future. Note, PCM don't normally fail without some help. Did something else "happen" during the work?
1987Stangman, this is not a PATS problem. The theft light is flashing because the cluster is not getting a valid signal from the PCM. This would happen if the PCM were not powered or bad. Remember that PATS requires a two way communication from the cluster to PCM for the 99+ model year.