On an 06 GT... Go whipple for sure! IMO, the whipple is the best s/c for those 3V motors, with the best potential! Its just a more solid unit. Less troubles with whipples than KB's. And if Im not mistaken the whipple runs a little cooler than the KB too. After all its a Ford Racing product.
BUT... The KB's do sound cooler than the whipples, if you like the blower whine anyways. You barely hear the whipple unless its wide open and in the higher rpm's.
Im probably going to buy a KB, but thats because they make a smaller one for my Mach 1, the whipple is just to much on my car!
In all honesty though its tomato tomato, apples and oranges. A twin srew is a twin screw! Youll love either one.