Charmon,
I have been looking into this whole aluminum polishing/ cleaning issue lately, and hear is what I have concluded.
A good aluminum polish works well if the aluminum is in good shape. Flitz is a brand that is often used. If the aluminum is in lesser shape I have been wet sanding the aluminum with 400 grit, and then polishing it back to a shine with a medium rubbing compond and an electric buffer (auto body style).
Everybody I have spoke with swears by a product called Sharkhide as a good sealer...
www.sharkhide.com. They also sell it at Stevens Marine.
For the paint, I think Motion Marine uses a powder coating process for their color. Try a medium rubbing compound and see if you can't lift the stain. There is a chance the yellow has permenantly stained the powder coating, if so you may have to live with it.
Good Luck...I think Mark, at Motion Marine, builds one of the nicest boats on the market.