Main Bearing Clearance

Exactly! Oil can take up a lot more room than you think. Without oil you may have .002~.003" clearance. And I agree with ramcharger's earlier statement that with your build you should shoot for .0025" clearance. Even .003" is fine. I wouldn't go any tighter than .002" for sure. Even though you say your not going to race it your description of it being a stroker that will make up to 600 hp and turn 6800 rpm that's an area that requires looser than normal bearings. Not as loose as a race engine but definitely a lot looser than a grocery getter. Don't worry about torqueing it down with no oil on the bearings. Won't hurt anything.
-------------------------------------don`t rotate the crank very much w/ dry bearings, and do it easily , makng sure their squecky clean if u do, better not to! Oil "will" take up some space if its in the upper bearing when plastigauging.
yup. I'll bet you found the issue. A "thin film" is probably .002" by itself. So clean the surfaces (backs of bearings and block/cap saddles) and try again. Don't move the crank once you lay it in place. Lubricate the studs, nuts, and washers with the ARP lube, torque in steps.
agree w/ this-----------------