That much custom work, go all out. Mount the inter cooler to the bottom of the hood with a Subaru style ram air scoop.
That set up looks like you'll have the space.
Or go nuts, and mount the intercooler(s), one or two small ones on the edge of the inner fenders and pipe them through the outside of the inner fenders with intake scoops on the fenders ... Something like these on the fenders ..
