Certainly can do one piston assembly at a time. That's how I'd do it. Write on the piston with a sharpie with the gap when done. That way you won't 2nd guess yourself that they're all done. I'd re-use the gaskets. write on them as well so they go back exactly as they were removed for best results.
Take your time removing the piston so nothing gets nicked. Use rod bolt boots/tubing & it's good to have a 2nd set of hands to catch the piston. Keep everything clean. Again, take your time.