Is the engine in / on the bike? Hopefully not. I would remove the side covers and get them bead blasted with glass beads and then repaint them with a rattle can of Honda Silver Cloud paint. Dr ATV / Beatrice carries it and one can will do quite a few engines. Your engine will look brand new afterwards. Just use thin coats and sand out any paint runs with 400 grit sandpaper and the engine will look great.
Unless your going for a concours resto, you could spraypaint it chevrolet bright orange if you wanted as long as you use high temp paint. Basically remove the engine from the bike and you should bead blast the covers. Myself I would only do the jug as it was steel and oxidized more often that the aluminum covers. I would beadblast the jug, spray it high heat black, scuff the side covers with 250 grit sandpaper or red scotch brite works good too and paint those a high heat silver. Then I would buff the innner round part on the alternator cover, buff the head, cam cover, tappet covers, cylinder head and engine cases. And clear coat the buffed peices.
You really don't need high heat paint,the head gets the hottest and you cannot find high temp clear.So since the clear holds up the silver on the cases will too.The cylinder is a different story tho and I use this ENGINE ENAMEL-Hirsch Automotive Products a can will last a life time and it might even be available in a spray,but I'm not sure.
I clearcoat the engine covers. Don't need much, just a thin coat is sufficient to make the silver a lot more durable...especially the added resistance to damage/discoloration from gas/oil/grease/mineral spirits. As for the center case halves, clear won't hurt anything but, it's better to just leave them "natural". As long as you clean them regularly, dirt won't build up, you'll prevent salt damage (ca chloride is used for dust control) and they'll remain unchanged for years.