If the crank has been machined to correct for the bend, then it would appear that the journals have been machined slightly off true centre for each journal, that's the only way you could have unequal stroke.

No amount of machining of pistons / rods will ever get it back in true balance, you may get equal C/R but you won't get equal stroke.

New crank required.

Maybe the machinist didn't know you would be checking stroke and maybe the tolerance is acceptable for a standard engine.

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