That (warranty) is my concern too. There seems to be a consensus that if your mod is shown to have caused the problem it won't be covered. This I think would mean it's up to Ford service departments to decide.
I asked my dealer about Ford Racing parts and he thought they would even cause warranty problems.
Maybe it's safe to do an intake (K&N) but keep the ability to return to stock?
Sorry to jump in on your thread with this.