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Bob good question. The down/power thrust(not talking back and forth) is on the caps more so then the block, so I would set all the mains to get the correct clearance. If there is more wear to the center cap from what I have read, I would not set the front and rear to .001-.0015 and leave the center at maybe .002+ by only taking off the same number of shims. As it is I have not really seen an engine that all the rods/mains needed the same number of shims removed for each rod or main when refitted. Without filing the caps, sometimes it is a compromise get clearance in the ball park, esp on a crank that is maybe a little worn or out of round.
Others may have different op, but this is what has worked for me.