The whipple goes for about $9G so I'd think there would not be too much diff in proce regardless of who offered it. The 3.3L 200AX (I beleive) would be killer on the GT500, but I will certainly wait to see what totally engineered packages are available. For example, a 3.3 whipple will want tube headers and bigger diameter pipes, flowmasters and possibly larger throttle body to fully take advantage. But then you're in the dilemma of tuning it for aobut 650HP ot up to about 800HP. Problem is the bottom end of the 5.4 with cracked-powder H-beams is about 650HP and you've already spent over 10G. And if you want to go further, you'll need to mod the bottom end. For about well under $2G you put pulley-kit and big-tube catback on, reflash the Oak and have the same 650HP for a small fraction of the cost.
So if I wanted to make this beastie into a 800+HP monster, the Whipple 3.3 is def the way to go, but up to 650HP it makes no sense to me, cool as it is.