Hey, I'm cynical from having to work with people with more cents than sense (but not by much). It's not directed at anyone specific here (usually, although I might make exceptions).
The theft light continues to flash for an extended amount of time
There's your problem. PATS is not proving out and the PCM thinks the truck is being stolen. Consequently, the PCM disables the engine.
Since you say you replaced the PCM, it's probably safe to say you did not follow the correct procedure in the workshop manual. Either reinstall the original PCM (if it is not defective) or tow it to a dealer for proper programming.
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