'The tightness HAS to be because of my shim removal.'
I think I agree.
So, you removed one .001 shim from one side of each main, correct?
That is the common way of explaining. we don't halve that just because we only removed from one side. I know what you are trying to say, but we don't word it that way.
So, the engine is still out of the car, and is upside down, correct? Meaning you still have easy access to the caps?
You said the journals checked out and were not oval, good.
Before putting the shims back I would re-plastigage all 3 mains (be sure to torque all the way, not just snug), record the readings, then rotate the crank 90° and re-plastigage and report the readings back. I believe you will find one reading to be too tight.
Very odd that the center main was the tightest, BTW. I am not sure what to make of that. Still have the original 64# FW on there? It is that heavy FW that makes the crank whip and eat up the center main first.
And you are saying there is NO movement fore and aft of the crank? Should be about .003 play.
Is it known how many miles on the babbitt? The thrusts on the rear main babbitt are OK, not cracked?
You are certain the front and center caps were not reversed during assembly?