Ford Repair: Ford PATS system, inertia switch, jumper cables

Question
Hi, I have a 2001 Taurus SE that I haven't driven in a few weeks. Unfortunately, even though the last time I wanted to drive the car I had to jump start it, I didn't remember to disconnect the battery(since I knew it would be a few weeks before I drove it again). Anyway, I went out to start the car & the battery was completely dead! I got the jumper cables out & hooked it up to my wife's car & charged the Taurus battery for a few mins. When I tried to start the Taurus, it turned over great, it just wouldn't catch.  I tried several times, even waiting a few times to let the battery keep charging.  No difference. The Taurus will turn over but will not catch/start.  We have had some severe rain the last couple of weeks so at first I thought it might be the cause of the problem.  And then I remembered a mechanic friend telling me that with Ford vehicles that have PATS(Passive Anti-Theft System),& that sometimes when the battery goes completely dead, the pats system will prevent the car from starting. He said you have to go to a Ford dealership & have them reprogram the PATS system and the keys again.  I don't have the money to tow the car to the dealer, much less whatever they would charge me to reprogram my pats system and the 2 keys.  Does this sound like a PATS releated trouble? Is there anything I can do to get the car to start?  I have not checked the fuel pump cut-off switch(but I will) since the car hasn't moved at all in a few weeks.  Any ideas?

Answer
A dead battery should not cause the pats system to lose it's programming. You will need to determine if the engine lacks spark or fuel, then proceed from there. Anytime you know a car will sit for weeks, it's a godd idea to either disconnect it or connect a trickle charger to keep it healthy. I have one on my street rod for winter, it's from Napa and was not expensive. I think it is called a Battery Keeper(?).

If the vehicle has not been moved, or hit by something hard enough to trip the inertia switch, that is most likely not the problem.