Horsepower Loss / Cooling Problem

How old is the block? Years of cooling system neglect before it was modded may have caused the engine to have partially blocked waterways. Your power loss may be stalled coolant in the intake manifold from lack of flow heating up the incoming air/fuel mixture so it's less dense and more vaporized. If this is a new engine/block, then it's more unlikely, but maybe this is a fresh idea. Hope you figure it out!