The mains have to register to the block, not the studs. Might have to ream the bolt holes in the caps? If the block is stock, the deck heights may be all over the place to where the piston to head clearance might be different front to back and side-to-side.
I like to have the mains align honed as part of the machining along with having the deck cut square to the crank centerline. I normally run about 0.040" piston to head clearance, and know other that run tighter than 0.035", but I don't want to push it. I don't pull the engine apart each season to check bearing wear.

I would not mill too much off the block/heads or the intake will land on the blocks end rails and the intake side of the head (or intake) will need to be milled to fit correctly. Besides, that much milling might cost almost as much as new pistons.

If using heads studs too, ream the bolt hole where the rocker arm oil supply flows too.