They dealership would have a hard time denying warranty with the mods you listed. I would keep your stock PCM to swap out before taking your car in for service. They cannot read what tune you have, but they sure can write a stock file over your Overkill one. That would be a bad thing.
Basically if something goes wrong with your car, in order to deny warranty, they would have to prove your mods caused the issue...that would be very hard in most cases, especially lightly modded.
Me I would swap PCM and throw the stock airbox in for warranty work. I no longer do this, as my dealership can see the headers, hear the lope of the cam, and there is always a few other visuals to be spotted.
