In my personal opinion...avoid Thunder for any mustang work you need. They are a great shop for F-bodys/GMs/and the like....but they are new to the mustang game. They are only in it because they have to be. They outsource a lot of the mustang work to another local shop here in town called L & S.
before I go on a long rant about L&S...StangHi is here in town. It is just off of Seigan (see link in my sig for the web site). If you think about it, stop in on the 13th, or any time for that matter, and chat with Cody. I am sure he will be quite interested in your car as he has an 05 GT with a saleen blower putting down just over 500 to the wheels and an 06 GT that he is wrapping up tuning that should put down roughly the same numbers.