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The blocks only have "repaired" in the filenames because they've been run through Netfabb, the "originals" would be identical except for some flipped faces and tiny holes in the mesh that cause really weird print errors.
It could just be a problem with your printer's tolerances, try measuring diameter of the cylinder bores and the pistons you've printed and then scaling up the pistons a bit before reprinting them to make up the difference?
I've never really had a problem with the crank but you may want to try the remixed version, others seem to have had better luck with that