HELP intake bolt holes not aligning

Here's some more food for thought..............

When I was guessing the shop cut your heads, it would have been the "clean up" cut to insure the heads were/are flat, I would like to hope they have an idea how much they cut for "clean up"

If you wanted to measure on your own, here's a way to figure it out. Go to the hardware store, get a shoulder bolt, screw it into a manifold bolt hole, measure from the shoulder to the bottom of the head with a pair of calipers, front and back, both heads, if you can lay your hands on a KNOWN UNCUT head, do the same measurement, and bada bing you can figure out how much your heads were cut.