All of the cylinders were originally painted, along with the cylinder head and center cases....silver or black. None of them have ever been just plain aluminum.
So.....clean it up as best you can, and paint it silver or black.
The outer cases (clutch and magneto) are somewhat polished with a shiny brushed finish and then clear coated at the factory- the clear coat doesn't seem to be very durable and it allows water to get beneath the clear and corrode the aluminum. Strip the clear coat and the outer cases (wheel hubs, fork yokes, etc. ) can be cleaned up nicely. I have been trying a lot of polishes to see which one is the most durable against corrosion - so far the Griot's Garage polish provides the best protection.....although I don't know why as it doesn't claim to provide protection. (I have an old pulley hub I polished up and leave setting outside in the driveway.....and the Griot's has kept the hub looking better longer than any other products I have tried).
http://www.griotsgarage.com/product/heavy-duty+metal+polish.do?sortby=ourPick...