Theoretically, you can do anything, but if what you do causes an issue or leads to something breaking, your warranty will not cover it. But everything is based upon if your dealership cares or not.
Go ask your service manager what mods they'll allow. Most dealerships are cool about cat backs and CAI's or drop-in K&N's. Anything else is pushing it unless otherwise stated by said service manager.
It is not a bad idea to discuss modifications with the SVT Technician at your dealer or at other dealers before you modify. Then you can decide how far you want to go, and what will be acceptable to the dealer. There is only one SVT Technician at my dealer, and he is the only one that touches the SVTs. I was discussing a regular service issue with my Technician and switched to the big what if questions. My Technician does not look for mods during regular service. More specifically, he does not look in the cage to see the size of the pulley, or at the SC belt to see what size, or at the computer to see if it has been tampered with, or at the HE to see how big it is. 50 state legal exhaust is acceptable, and aftermarket intakes are OK (unless a recharged filter causes a problem). If there were a major service issue, then Ford would be looking for a cause (get it back to stock). After talking to him, I was comfortable with the mods I was considering, and know what is acceptable in case of a major failure. It was nice to be able to make informed decisions about my mods, and I am not loosing any more sleep over my warranty.
my buddy bought a new 2002 z28 and they voied warrenty for an air fuel gauge lol they sai it broke the trans i couldnt stop laughing thats the stupidiest thing ive ever heard id ask the tech good luck bro
Sticking with Ford Motorsport parts will be OK, too. Like the FR500 cat-back or headers. As long as they are properly installed, Ford would look pretty stupid voiding a warranty for their own parts. In fact I think one of their selling points is that they will not void the warranty as long as the engine isn't opened up.
I just had mine in to replace the rear main seal, plate and slinger assembly - slight oil leak. There were absolutely no questions concerning my mods, which inculde Steeda UD pullies, Steeda shifter, FR500 cat-back & K&N.
But, experiences can be different and I've seen some pretty lousy "calls" by service managers.
IMO you should be safe with a CAI (you can always change it back easy if its an issue), shifter, catback exhaust, tires and subframes. You can change the midpipe if you want, but if you are warranty concerned I would get a catted version unless you want to take it off everytime you go in.