I had the same issue with my 03 F150, would crank but not start with the theft light flashing...

The problem turned out to be a bad ECM relay that was not powering up the ECM

Considering you cant pull the codes, i'd be checking your fuses over and also you might try swapping the relay that powers your PCM or even the PATS module (if it has its own relay)

Edit: Just reread where you checked all fuses and swapped the PCM relay. Not sure if there are any other relays that might be of issue..
2nd edit: I dont think its a bad key issue since it died on you. I could be wrong but I think that once the PATS has verified the key, it no longer controls anything. If that module loses power on the other hand, i think it could cause an issue.