I had a Rouscharger installed on my 2012GT a few weeks and here's the thruth about the warranty.
The kit that are labeled as 540hp come with a 3yr warranty if pcm is programmed by Roush and installed by certified tech. All powertrain is warrantied.
Tuner kit only have a 1 yr warranty on the supercharger itself
The 575hp kit just came out and yes it has a basic warranty with it but if you want the full 3yr warranty for the powertrain it will cost you 375$ more.
The 3yr start with the delivery of the car not the date of the supercharger install.
I have just purchased the upgrade kit from 540 to 575 hp which is supposed to give better low end torque and throttle response and got it for 325$ from Roush after negotiation.
This upgrade kit maintains my 3yr powertrain warranty.....if i stop modding my car....
BTW i am really mot happy with the result of the 540kit with the Roush tune so lets hope that the upg kit is better or i'll tell warranty bye bye..