Damon and fellow vanagon types 
the main bearing do crush as the case is bolted together and the crank clearance change as the engine heats up. The best method of checking clearances is to bolt the block together and use a good bore micrometer and then compare the numbers to the crank size.  If you case measures no wear on the split main bearing saddle the you only need to worry about the case shift. This can be tricky stuff as the only main bering you can plastigauge is the split center main. The rear main bearing needs lots more room than the .001 to 002 ths you suggested try .003ths plus 
anybody can reassemble an engine but correctly rebuilding an engine requires alot of measuring 
Damon call me if you need to I am around this week end 

Bob