Mixing already bored cases is not a good idea. Unless the cases are an almost exact match, then the re-boring will result in an oval hole in one or both cases. You could try filling one or both sides with a low temp alloy weld before re-drilling and boring but best solution is matched cases. Simple re-boring might work but might not. Have known of cases where it has worked (usually singles) and times when it has not.
May not be necessary at all, as the mains are ball bearings and factory tolerances are such that you will most likely be within alignment spec. On a unit 500, I'd be worried with the timing side bushing.
Install a new set of mains, install the crank, assemble the case halves, torque them down and check your free rotation. This basically costs you nothing extra, and you'll know right away.
Cam bushings are a different story, and should be reamed in place (preferrably using undersized bearings so you have plenty to work with).
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