You only need to use assembly lube when dealing with cranks, rods, cams and such (the "hard parts" in your engine). Replacing which gaskets? There's a few... If you're lapping valves, then it's safe to assume you have the head off, so replacing the head gasket is wise, the valve cover gasket, and while true there, the rubber pucks between the ad and valve cover (they cover the head nuts) are best replaced. Use a little Hondabond to seal those.
If the carbs are off, there's an O-ring behind the intake manifold that is good to replace, but you'd be well served to download the manual here:
http://manuals.sohc4.net/cb550/ and perform the listed 3,000 mile service interval.
Any other information you can provided will help us guide you through- like year of your bike, and whether there are any modifications known from stock.
Welcome, by the way