The engine was loping, that is, the idle was fluctuating by about 1000 rpm up and down. I changed the mass air flow sensor based on advice I found here. That wasn't the problem, so I changed it back and changed the air filter while I was at it. The Haynes book says the air and fuel filter can cause idle issues if either one or both is stopped up. It turns out both of them were.
My mechanic believes the Pats 2 system may have caused the stumbling and loping. I disagree, I think it was the filters.
Certainly either one of us could pull the battery cable to clear the body codes, but with it we lose engine parameters and fault history. I'd rather clear them the right way.
In any case, something is messed up inside the driver's door making it so the perimeter alarm won't set, also the electric lock doesn't always work. I have flat metal keys with no transponder in them that can turn the ignition switch (no way I'm paying $50 for a spare key in case I lock mine in). The very first time I stick one of those in and turn it, it'll set that code again. It'll re set the codes for the driver's door.
I didn't know it could even store codes for this stuff... If I had I would have learned how to pull them so I would know why my alarm doesn't work.
What I need to know is can the anti theft system shut my engine down in mid flight. I've messed with a couple Explorers with this system, the only things I've seen it do is prevent the engine starting, flash the lights, and blow the horn. I've never seen one kill an engine mid stride like that--if it's anti theft related, everyone I know of who's had it had to have the vehicle towed to a shop. I drove mine in.