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You didnt oil the back of the shell did you?
Does the crank have that free movement feel if you make a very small rocking action with the crank?Do you have any doubts that the crankcase halves were a factory pair?
When you assembled the crankcase halves is it possible that an excess of Hondabond could have entered somewhere to lead to this problem? Could the crank seals be somehow causing the extra binding if they have distorted?I'm assuming you have not fitted the block yet.I think you will have to split the cases again to investigate further.