I may be in the same situation. I recently bought a used 07 GT500 with the Shaker 1000 and it doesn't sound as good as the Shaker 500 in my 06 GT. I was wondering what's up with that? After all is like a $1,200 option.
I've tried adjusting the base and treble, turning the subwoofer on and off, but it just doesn't sound as good as the Shaker 500.
I hope we get some suggestions on this.