Intake alignment Q

So i have a 68 440 im working on, it is in a 83 ramcharger but that is irrelevant to this question. I bought the truck with this engine in it with a bent pushrod and valve. I tore down the engine and had the heads rebuilt, now im putting everything toghether and im having some issues with the intake lining up. With no valley pan the intake matches and bolts go in easy. Withe the valley pan and paper gaskets it does not. It almost seems like the intake is hitting the valley pan, i used the felpro pan. this is the same intake that was on the engine before and i did not have the heads cut. Could i have used a different thickness head gasket and its throwing it off? any suggestions?