That's a good idea to suspect PATS and try a tune with it disabled. According to my Centennial Owner's Guide the THEFT light should "flash rapidly or glow steadily when the ignition is in the RUN position". Have you tried a different ignition key? I have a non PATS key for my 2000 Sport. When I use the key the starter cranks but the fuel injectors are disabled. However, if I spray starting fluid into the intake manifold with the chipless key the engine will start and run for a few seconds proving the ignition is not disabled. There's a DTC associated with PATS: P1260 Theft Detected - Engine Disabled. You didn't post that DTC as being present. Below is something I found on the internet:
Question:
I have a 1999 Ford Explorer. The car doesn't start and when I retrieve codes I am getting a P1260 - Theft Detected, Engine Disabled. What can I do about this Ford engine light code?
Answer:
Thanks for contacting us with your Ford engine light question. P1260 indicates that the Passive Anti Theft system (PATS) detected a "theft condition". This basically means an incorrect signal, or no signal at all was received from the chipped key. Brief overview: your ignition key has a chip in it called a transponder that is read by the PATS transceiver (mounted around the ignition cylinder housing behind the column shroud). The signal is then sent to the PATS control module, which communicates with the Powertrain Control Module (PCM) and enables the vehicle to start. Sorry for all the acronyms! When an incorrect signal is received, the PATS module then sends this message to the PCM which triggers the P1260 trouble code, resulting in a no start condition. Possible causes are: an incorrect key being used, faulty key chip (transponder), wiring concerns between the transceiver module and PATS module, the transceiver module itself or internal PATS or PCM module concerns. The first thing to do in this instance is retrieve codes from the PATS module and diagnose these. Once the PATS issues have been resolved you can reset the P1260. Communication with the PATS module will likely need to be done at a Ford dealer. A few things to check first: make sure the correct key is being used, and if you have a second key, try that one as well. If one key starts it but not the other, you may have a faulty key. If both keys do not work, then it is not likely a key problem. Honestly, we see very few problems with the keys themselves. Make sure no one has tampered with the steering column shroud as the transceiver module located behind it is fairly fragile. Lastly check for an aftermarket remote start system. These are a common cause of no start problems with PATS equipped vehicles. Some installers will remove the chip from your key and tape it to the column (under the shroud). This basically bypasses the system and allows it to be started without a chipped key. The problem is that the transponder removed from the key is not designed to be used in this way and can fail due to extreme temperature changes and, depending on mounting condition, excessive vibration and shock. Other installers use a "key box" installed under the dash, and these have been known to cause issues as well. If you suspect the concern to be related to a remote start it may not be a bad idea to have it checked or removed to complete diagnosis.
