Horsepower figures fell off slightly in the last SN-95 Mustangs because the new "bar of soap" styling didn't leave enough room underneath the hood for the original intake manifold. Even if the donor 302 came from a SN-95 Mustang, there's more than enough room under the ST hood to use any factory or aftermarket manifold. There are plenty of bolt-on manifold choices that will work with the factory EFI, and range from long runner designs for more low-end torque, to straight shot all-out drag racing designs. For a relatively heavy ST, and with the oversquare 302 bottom end, you'll want the torque, trust me!
If you want a real challenge (and an almost certain divorce), see if you can find a wrecked Lincoln Aviator, and drop in the 4-valve mod motor from it into your ST. Bone-stock you'll be getting 302 BHP and 318 lb.-ft., a lot more than any stock 5.0 of that vintage. And the bottom end is good for twice that if you want to add a blower. :bwahaha: