It was certainly not the intake's fault. That intake manifold will support 600 hp easily. Could have been the camshaft, could have been a number of things, but it's very typical for an engine to produce more peak torque than horsepower. My guess is was the fault of the Shelby heads.
Nobody uses Shelby heads because they are not performers and you have to pay for the name. They flow about what an Edelbrock head flows....about 270cfm. They're down 60 cfm to a Trick Flow head.