So after a bit of research I found out that a lot of other people have had problems with the exhaust crossmember brackets rubbing and making noise, and that on the 07-09 mustangs the brackets are not there at all and the exhaust system is only held my the exhaust manifold bolts and the rear mounts.
Anyway on my 06 GT the left hand bracket was rubing like crazy and driving me nuts, so I cut that sucker off and the sound is gone
What do you guys think of what I did?