The problem is not the actual clearance measured by the hole diameter vs stud diameter. The hole in the cap may not be consistent and it could be because the stud is not straight after seating in the block. It is very common to have problems when using studs. A bolt will not seat in the hole like a stud will. Think about it. The whole area in the block is threads and will come STRAIGHT out. A stud will not. My Machinist reamed out the holes in my main cap using a reamer. Makes a smoother hole but a drill would be fine. You have nothing to lost by drilling the hole one size larger. I bet that fixes it.

OR you can try intalling the cap temporarily with a BOLT and see what that does (re measure). If that fixes it then drilling the cap hole larger will almost for sure do it.