I solved the problem. I'll write out the steps I took in the event this might benefit another member in the future with a similar problem.
Contacted American Muscle, which in turn contacted SCT. I requested to have PATS disabled in my two custom tune files. SCT tech emailed me two updated tunes with PATS disabled along with instructions on how to upload an email tune file into SCT XCal2 using a free to download software called LiveLoad Ford 220.127.116.11 from sctflash.com The updated tune files were free of charge as part of AM's lifetime tune policy.
My car would not start prior to this process due to PATS P1260. And this is probably due to either a bad transponder in both keys, bad transceiver ring in ignitions switch, or a bad diode in PCM. Or maybe another problem as well. Who knows. And I don't care as I'm not going to pay to have this crap diagnosed and fixed at the dealership. I've got better things to spend my money on right now.
1. Disconnect battery for 1 hour.
2. Pump the brakes to bleed off any excess voltage in the system.
3. Reconnect battery
4. Plug in tuner to OBDII port (with key off) and begin program process of uploading new PATS disabled tune file, following the prompts. Complete that process.
5. The car fires right up. Theft light does continue to blink intermittently, but not in a fast pattern like it did prior.
6. Run DTC scan and the P1260 is gone, but you do get a P1000 readiness code.
7. Follow the instructions on going through the Ford Drive Cycle process to address this code. http://www.obdii.com/drivecycleford.html