Ok, so no fuses out, still stumped on why the locking system is not working with the remote fob, but the engine immobilizer is.
I cleaned the MAF, the MAF housing c-clamp had fallen off so it was just kind of hanging loose on the rubber intake boot. That sure wasn't helping.
Also found this vacuum connector leading no where. I'm sure it is supposed to lead somewhere, any ideas? Couldn't find any other loose stuff.
Seems to be running better now, but for whatever reason it only lopes when the air temp gets down below 50 degrees or so. I'll try it in the morning and see if its still doing it.