I don't use those heads so I have no experience with them. On other brands, there are manufacturing tolerances involved, and yes, you can get some stud holes that go through and some that are blind.
I wouldn't tear into anything at this point. I would simply buy/rent/borrow a bore scope, shove it down the intake manifold, and see if you see
oil anywhere.....in the runners, on the backs of the valve heads, running down the guides, etc.