Will a 2011 Mustang GT exhaust fit a 2006 mustang v6?

They SHOULD fit, problem is that the '11+ GT used a sort of ball & socket flange at the mufflers instead of the slip fit that the '05-10 cars had. So you will have to either cut those off the over axle pipes and figure out how to make the slip fit joint work (probably by adding an extension piece), or cut the flange off those factory mufflers and have it welded to your Pype bombs. Main problem would be getting the length right. An exhaust shop could probably make it work though.

You may have to cut the pipes before the axle to get them into the car. They are so long they pretty much have to either be cut or be installed on a lift.
At any rate, it's the same chassis so I would think they would fit, otherwise.