I see what you mean about the crank mark. I actually did it by looking at the valves and then measured, and then moved them and remeasured to see where they changed size. The heads were shaved and the block was decked. I'm not saying that i don't still have a vacuum leak but everything seemed to start working better after i retorked the intake. It's getting there.
OK, well how much were the heads shaved and how much was taken off the block? If more than a certain amount, and especially if not done at the proper angles, and the intake was not machined to match, that could cause intake sealing problems.
If the intake angles are not right, then you may well be fighting this over and over. Here are pix of how well matched the intake and head angles are on our build with new heads and intake; these are prior to any torquing of the intake bolts, and on block decks no more than .002" from square to the bores vertically and pretty much perfect-on horizontally.