If the heads have been milled at some time, it's possible that the intake passages in the heads and the manifold aren't lining up right anymore. Are you using a stock intake, or something aftermarket? It's not uncommon to have to mill the manifold-to-head flanges and the end gasket surfaces to make a manifold fit right, especially if you're dealing with angle-milled heads and/or an aftermarket manifold. It's usually necessary to take 3X the cut from the ends that is removed from the sides when fitting a manifold.
Try putting the manifold on the engine without gaskets, and see if you can slip a feeler gauge between the manifold and the heads anywhere. There should be no gaps on a properly-fitted manifold.
Jerry
