The fix or to put it more accurately, the work around:
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 and runs great.
6. The theft light may or may not blink intermittently for a while after starting, but not in a fast pattern like it did prior.
7. Run another DTC scan and the P1260 is gone, but you do get a P1000 DTC readiness code.
8. Follow the instructions on going through the Ford Drive Cycle process to address this code.
http://www.obdii.com/drivecycleford.html
9. Done