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I agree that that will give you an accurate measurement , however its only accurate at the center line of the cylinder-if the block has ANY tip/angle to it at all from the 90 degree------ like for...

It your scenario you basicly have to assemble the engine to take measurements to the oiston but basicly you don't have a deminsion to which to deck the block and you still don't know what the deck...

If there is a difference in cylinder to cylinder you can off set bush the small end of the rod without any further balance issues unless its an aluminum rod and then there will be a small...