Almost every exterior surface of the engine is painted. The jugs and cases are painted an aluminum color, and the valve cover, stator cover and shifter cover are clear-coated, IIRC. The easiest way to clean up the oxidation on the clear-coated parts is to strip/sand off the clear and then polish them. These parts will then need to be polished on a regular basis to keep the oxidation at bay.
As for the jugs and cases, once the oxidation gets underneath and the paint starts flaking off, the only way to actually clean it up is to repaint. If it's only really bad in certain places then you can get away with spot painting if you find a good match.