Rapidly Flashing Theft Light

[pullenr]

I am having problems with my 98 3.8L Mustang starting occassionally. When I insert the key into the ignition and turn it to start the theft light starts flashing rapuidly and the engine will not turnover. Most of the time if disconnected the battery and reconnected it the car would start. I replaced the battery after the original was tested and found to be bad. This seemed to solve the problem, but yesterday I took it to a muffler shop because my headers were leaking on the passenger side. When they tried to start it to drive it into the work bay the same thing happened and now it will not start at all. I tried everything in the manual and even disconnected the battery, but to no avail. I have a performance chip in it, dual exhaust with mac headers, flowmaster mufflers, forced air induction, and underpulleys. Any advice on what the problem may be and how to get it started would be appreciated. Thanks.