So you probably did have a tune, and now that they found it, you're pissed Ford won't pay for your engine damage? If they found something in your PCM, it's because something was there... They don't just make shit up. You work for Revolution Performance and you've raced the shit out of everything else you've owned. You really left your car stock? Not likely.
And, all this talk about your "source" who knows someone at Ford sounds BS to me. It's hearsay at best. We've sold a bunch of early build 5.0's and haven't had a problem with any of them that were left stock. If there were a problem with them, we'd see more of them fail. As it is, it seems the only ones failing are the ones that are modified, or have aftermarket tunes on them.
If your car really was bone stock, then you should get an attorney. Since Ford found some sort of evidence your car was modified, you probably already know an attorney would be a waste of time.