340 misfire

Ok, that will be the next thing I do. When I put my new manifold on, it didn't want to bolt on very easy, and when I got it on, the front didn't make contact with the cork gasket on the front of the block. I could fit my fingernail in the space between the intake and gasket, so I put some rtv on the top of the cork to seal it. Could the heads be milled causing the intake not to fit right? I bought the car almost like it is, I just swapped heads and intake so I don't know. I can't imagine since the stock rocker arms are being used. If so, could that cause it?