On this block, this is how much the stud sticks out through the
nut, and is being measured with calipers, (no washer) and needs to be shortened so it is
flush with the top of the nut.
If you want to go the route of removing the top threads from the
block you really need a drill press (pillar drill in England) or a vertical type mill.
Use a 15/32" drill, and you MUST have a stop of some sort set up to control the depth
accurately.
In actuality only the end mains need to be done.
This is what you are looking for, studs flush with the top of the
block.
If you have a lathe, then this is the easiest and most accurate
way to do this job.
Put the block back on the gearbox and mark the area on the webs
which need to be relieved.
The front web is a little more tricky to get at, but you can mark
the inside OK, and then mark the other side later.