I'm betting the only difference between the two is its' subwoofer output. With my sub turned off, it sounds like the stock Mach 460 in my 03 cobra (which isn't that great).
dont get the Shaker 1000, get a good after market, Pioneer, Kenwood something like that, the speaker system isnt bad, but the shaker unit sucks, you wont believe the difference with a good head unit.