My tuner told me they also pull timing when AIT gets really high.
Either way, pull those plugs and change them, cheap easy good maintenance (lucky modular guys)
As already stated check for liquid, etc. How long did you drive it without a filter? If you are saying the problem keeps occuring is the check engine light, then change the o2 sensors. They probably haven't been done yet, and at 100k miles it not a bad idea. Get motor craft ones. I got bosch ones and they suck. When i go back to the dyno I am buying motorcraft.
I don't imagine you encountered anything you won't be able to fix. Our cars are pretty easy to work on.