Trickflow/Summit response:
how tight are the studs in the block. A lot of people think that you have tighten them until they bottom out in the block and that is not the case. They should be tightened until they bottom out and then loosened a half-turn. If you tighten down until they bottom out, it will throw the stud on an angle, especially the longer studs.
We have also ran into a stock block durning R&D to where one of the holes in the block was a couple thou off, which made the longer stud even more off on the nut side.
I've turned a piece of stock to .500" on one end and .5285" on the other. The bolt holes are .530-.531" in the heads. I'll chuck my tool in my drill press, mount my head to a piece of plywood for easy clamping/holding ability, locate the head using the larger end of my alignment tool while it's chucked in my drill press and clamp it to the table. Then replace my tool with a 35/64" (.546875") drill bit and open the hole up. Only issue I can forsee is my tool I made may be too long causing a need to adjust the table height in otder to switch between centering tool and drill bit. Worst case scenario I have to shorten it.