This sure sounds like a PATS issue to me.
What is the theft light doing?
Are you sure there aren't any vacuum leaks in the upper intake tube?
Have you confirm that the fuel injectors stop pulsing? If so, this adds weight to this being a PATS problem.
If you want a wiring diagram, I can help with that. PM is interested.
2003 GT Convertible (sold & missed)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.