Just a check, you made sure the bearing saddles in the block and main caps were squeaky-clean with no oil or dust/debris of any kind, right? Anything in between the bearing and saddle can give false clearance readings. Same goes for crank journals, give them a wipe down with lint-free cloth/rag with acetone and blow them off with compressed air.
Also gotta make sure all main caps are torqued to the same spec, noticed you didn't do that... When I recently plastigage'd my 440's mains I put a piece of plastigage on top of each main journal then torqued all the main caps fully to spec. With original factory crank very lightly polished, new standard-size Clevite bearings and original main caps the plastigage was just in the middle between .002 and .003 so I called it .0025 and moved on.