There are some aftermarket gaskets out there to address this issue. They are available in various thicknesses and you can also try a gasket on both sides of the valley pan.
The fel-pro gasket set came with 4 paper gaskets and a metal pan. I cant use the 4 gaskets with the pan because i cant get the bolt hold to line up. The bolt holes line up perfect with the paper gaskets with just the metal pan.
I have a hard time believing that fresh heads from a machine would be off square.
The intake I have came off this motor with different heads. I dont believe that the intake has been milled and the heads have not either. With that said, the way i checked the intake for square or warpage was i held a flash light on the opposite side of a straight edge and i looked for light to come through the bottom side of the straight edge while skimming it across the surface. Nothing came to my attention while doing this.
Is there a more appropriate way of doing this? Im trying to stay out of the machine shop as the one i use is VERY credible and wants an arm and a leg to do anything.
I dont want to order a new intake until i am positive thats the problem.