The dark "stains" on the aluminum is probably smut. It is caused by the different elements in the alloy of the Aluminum, most notably, copper. The stain is hard to remove by polishing. Wet sanding will remove it. Most people will polish the engine covers and paint the case, cylinders and head. Trying to polish between the fins of the cylinders, I think, would be an endless job and very frustrating. Any tool you can find or make that will fit between the fins isn't going to be big enough to process any meaningful surface area quickly. Think of trying to polish something the size of your gas tank using the tip of a pencil erasure. It ain't going to be quick!
Your best option is to clean all grease off and prep the surface with fine wet/dry sandpaper or soda blast it before painting. Soda blasting is very messy and you need to be absolutely sure all possible entry points into the engine are sealed tight.
-P.