What Oil Clearance on Mains?

Why would you need to torque up all the main caps unless you're checking them all at the same time?
What undersize is the crank?

Could potentially push the crank up/down on one end, not likely but 0.001" is a tiny distance to be considering on something that's 2 feet long and 6 inches around. Torqueing fasteners in general also just does weird stuff.