Ford could not "void your warranty" even if you told them you had tuned the car. The Magnuson-Moss Act requires the dealer to prove that a modification you made caused the part failure which requires warranty work, and even if it did, they cannot void your entire warranty because of a modification. They can only refuse to fix under warranty a part that the dealer proved to have failed as a result of your modification(s). The dealer would be standing on fairly solid ground if your motor blew and they refused to work on it, but for things like cracked leather seats and rattling AC vents, there is no way the dealer could prove a tuner made them break. I would still recommend putting the stock tune back in your car, just to be safe.
Disclaimer: I am not a legal expert, so don't take what I just said as gospel.