I lay the intake on the heads with no valley pan or gasket and take a feeler gauge and measure how much gap there is in each corner, top and bottom, front and back sides and write it down on the manifold with felt tip marker so I don't forget or get confused later, I also look at the manifold bolt holes and how they align with the bolt holes in the heads and go from there.
Once that is done take the manifold to a good machine shop and have them cut the intake to remove any angle and get clearances the same on the entire intake the same
You may need to have them remove some additional material later once it is straight on the heads to get the bolt holes align properly also
I like to see zero clearances on the bottom(all four corners) with no valley pan or gaskets and maybe up to and no more than .003 clearance at the top all the way across so the intake pinches the bottom up tight against the valley pan and or gaskets
IHTHs