Ford Repair: 99 Mustang THEFT Wont Start, random intervals, auto terms

Question
My husband bought a used 1999 Ford Mustang. He began having trouble with it starting. We took it to the mechanic - new almost everything - brakes, battery, spark plugs, you name it! Now, it runs great, when we can get it to start. I think it has something to do with the Passive Anti-theft System. We had two brand new keys made and programmed at the Ford dealership in hopes to fix this problem - to no avail. At random intervals, if you go to start the car the THEFT red light will flash and continue to flash and the car will not start; it will crank but not turn over (forgive my ignorance in auto terms). All the electrical stuff works - radio, lights, etc. Most times, you can leave it sit for 30 minutes, come back and it will start right up. (Needless to say, all the waiting is very frusturating! Always happens at the most inconvenient times.) Well tonight, it will not turn over. We've tried three separate occasions of one hour intervals trys. Is there a way to simply turn off the anti-theft system to stop this from continuing to happen? Is there a way to reset the theft system to get it to start? A way to trick the THEFT system? These are both new Ford dealership keys.(The dealership says they should work fine.) The car should start but it's in THEFT limbo. HELP please or point me in the right direction!!! I greatly appreciate any assistance you can give.  

Answer
Shanna-

  Unfortunately I don't have a lot of experience with anti-theft systems.  To be perfectly honest they've always annoyed me so I never bothered to learn much about them.  I'm pretty sure disabling it is as simple as pulling a fuse...that would sort of defeat the purpose if all someone had to do to steal your car was pull a fuse.  If I were you I'd take it to the dealer who gave you the keys and basically tell them "it's your problem now".  Well...ok...not like that, but explain the problem to them.  They should either be able to disable, remove, or reprogram the anti-theft system.  If it's so intermitent I would imagine it's just some sort of glitch or else you'd be looking at a car that never started.  Hope this helps.

Steve