Those Shakers (at least the Shaker 500's) are notorious for having issues. I had mine replaced by the dealer because it was skipping, and there was a TSB out on it.
Is your car still under warranty? You might be best off taking it to them and having it replaced.
This says it's just for 2005, but issues have been known to go beyond what they state in the TSB:
http://bradbarnett.net/mustangs/gala...sb05_10_19.pdf
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2005 Mustang GT in Torch Red
C&L Cold Air Intake/Diablosport Predator Tune
Tokico D-Spec Shocks & Struts
Steeda Sport Springs/Front and Rear Swaybar/Front Swaybar Brace/LCAs/Adjustable Panhard Bar and Brace
Steeda-branded Borla Stingers
Steeda Underdrive Pullies
1965 "GT" Logo and some other chrome bits