I was informed by a reputable tuner that these modern PCMs have a permanent memory log that cannot be cleared, even by Ford. That's the whole point of this stategy - no way to hide the history of changes to the programming.
To the OP: I feel your pain, and the dealership WILL repair your car, just not under warranty. Why not take it to a tuner and have them go over it? This will probably be cheaper, and avoid further "history" with Ford... just a suggestion
Paul
The PCM has a field called date last mod, which shows how many key cycles and the date the last time the pcm was modified.
What I am saying is, since the OP had a tune but reverted back to stock, his "old performance tune" should have nothing to do with why he is having issues now.