There are several products available specifically for cleaning and polishing polycarbonate, such as our headlight housings. One in particular I'm familiar with that's used quite a bit in the aviation industry is the Autosol brand. Unfortunately they're updating the web site or I'd post a link, but you can find their products at places like Sporty's Pilot Shop or your local FBO. Another product I've heard good things about is from Craftics, where they have several polycarbonate items. Also just found out about this product as well: Novus Plastic Polish.
Just be sure to test whatever product you choose on an inconspicuous area (the underhood portion behind the seal) and follow the directions, especially regarding the type of polishing cloth and keeping it clean. It will require slow, patient work but the right product for the job makes all the difference.
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