02 X - V10 heres the story:
I bought this used 2 mo ago, worked fine. Got to tow RV. There were no tail lights at trailer plug, that isn't the issue here, but what may have led to my problem. I was trying to trace down the wiring, under the chassis are 2 plugs near the Trans - they have wires for the rear lights on the Truck as well as wiring for the Trailer plug, and i think a few other wires for ? I accidently shorted a wire and got a spark. In the end i fixed the trailer tail light problem, but, when i went to start truck, anti-theft flashed rapidly, truck would crank but not fire. Towed it to Ford Dealer #1. Told them what i did. They said PCM was fried and replaced it. They told me problem of not starting was solved, but the anti-theft light still flashed and they didn't know why. I paid them $1300 for PCM and 6 hours of diagnostics and they gave me back a truck not really fixed.
I can start it, it runs, but the anti-theft light flashes fast for 40 sec, then gives a 1-6 code. The truck starts with a cut and unprogrammed key, the fob will not program (turn key on/off 8 times and nothing at all happens). Took to 2nd Ford Dealer. They said new PCM was bad, but, dealer 1 sold it as a Ford Part, which should be warranted by all Ford dealers. Dealer 2 says it isn't a Ford part, Ford don't make them any more, and so they insist dealer 1 must pay them to swap out a new PCM. Dealer 1 insists the PCM is not bad so they aren't cooperating.
What else could i have blown out when i shorted some wire in the plug under the chassis that could be confusing the PCM (and the dealers), or if it is a bad PCM why won't the Ford dealer 1 cooperate? I will be calling Ford's customer service later today.

 

Maybe resolved.
After days - weeks - the tech at dealer #1 kept insisting the problem was due to my truck having diesel gauges (I think he's been breathing too much exhaust), finally he and the tech at dealer 2 talked today. The conclusion is dealer #1 put a PCM for the F-250 in the Excursion. The 250 didn't have the PATS alarm until 07, but the excursions had them. So, the PATS fired off the theft light and lets the car start with non-programmed keys and won't program my fob. They are sending out another PCM made for the Excursion and the PATS alarm... As far as I can tell, it all makes sense now. Hopefully this will resolve the issue. But, the tech at dealer 1 should either be sent back to Ford school, or shown the door. It appears he couldn't figure out way the anti-theft was flashing and why the PCM wouldn't communicate with the PATS and made up a story, lying to his service manager that the problem was with my truck, that I had an instrument panel for a diesel in my V10 truck, saying that was why the light was flashing and he couldn't make it stop... What a looser.

 

I just had a similar issue and had to replace the alternator and the batteries. I guess the batteries had some bad cells and messed up the altinator that made the theft system activate.