If you are talking about the cdc shaker system the difference is that the 07 and up came with the factory hood scoop I beleave and the trim ring that comes with the shaker will not cover the holes left from the faxctory scoop. THis sucks for me cause Iwant this system bad but its going to cost a **** load of money for the cdc alumnium hood wit hthe cutout flange and the shaker system. Bye the way cj pony parts has the shaker system for like 750 this week only they are doing 10 percent off it was like 800 but as usual I have no money.
Well the 05-06 is for gts from the year 2005 and 2006 and the 07-09 is for the years 2007, 2008, and 2009.
There are just a few minor changes to the engine bay that requires different mounting material in the later years; no noticable differences in the kit however.
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2006 V6 auto with the pony package
adding to it everyday
the difference is in the tube that runs fron the CAI box up to the Shaker base is different. the 05-06 GT's have to have a notched tube where as the 07-09 dont.
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Saleen S/C 3.2 pulley tuned by JDM Engineering, GT500 pumps, CHE goodies on the rear, 4.10's, KOOKS/ high flow catted X pipe with PYPES Violators, Spydershaft, TCI 3500 stall, PA deep tranny pan. Meziere w/p,M&H 325/45/17 DRs.
future mods.... a 3.0 pulley
whats the difference between the 05-06 and the 07-09 Shaker systems 
