Putting in any of the above may cause a dealer to refuse to treat your repair as a warranty issue. Alternately, doing all of the above and telling your dealer about it might still not cause him to turn down any work as warrantied. It is entirely up to the dealer, once you mess with the car, you are taking your chances.
In theory, you have voided all warranties that have to do with the parts you replaced or damage caused by your replacement parts, and, again in theory, nothing else.
In practice, dealers do what they want, and unless you are willing to commit a large amount of time and risk a large amount of lawyer fee and court cost money, you aren't going to be able to fight that.