micjulmic, a Magnaflow is a wonderful muffler, I love mine! Definitely get the Y-pipe as well. As for intake, I'm very happy with my aFe Stage 2. I've really considered shorty headers but I can't make up my mind. Since you're a 2010, a diablosport predator would be great!
To be 100% sure, I would contact your local dealer. But normally it won't unless the muffler was the reason for failure. I checked with my dealer about modding and warranty, and you can do most of the safe bolt ons without voiding warranty. I'll think you'll be fine if you change your muffler.