When I had a flywheel resurfaced, the machine shop remove the locating pins, and returned them 'loose' if memory is correct. I then just placed them, and drove them into their abode with a hammer. Seems to have worked. Only one concern with replacements is their source and quality, so I guess that's two concerns.
If you do replace with new, be sure to clean the surface of any 'preservative' coating that may have been applied. I'd use brake cleaner along with a lint-free towel/rag, etc. Also, be sure to keep the clutch disk friction material free of greasy thumbprints. A few likely will not hurt overall, but you don't want to get oil/grease/contaminant on the friction material, or you'll be back under there again.
tom