It should go in with just the metal pan and great stuff in the corners.

I know you said that YOU did not mill the heads, block, or intake, but it sounds like some milling on something was done in the past to give you the problems you are experienceing. You may want to have a few thousandths shaved off of the intake to make it fit well because you may get her to bolt on to the motor okay, but it doesn't need to be off much to suck oil into the intake runners and give you a vacum leak...I know this from past experience BTW.