If it's tannins, like from a lake or river where lots of leaves make the water a darkish color, you can remove that with muriatic acid. Wear those long kitchen gloves and goggles, as this is an actual acid. Be careful dripping it on anything metal, as it'll eat it. It won't react with stickers or plastic though. Just wipe it on, and then rinse it off after a few minutes. The stuff is pretty cheap, like $7/gal from home depot (in the chemical aisle).
If it's just a surface stain, you can try buffing it out. I've gotten stains out by rubbing it with a wet rag and baking soda. You will need to buff/polish the hull with an automotive or marine compound anyway, but I'd try the acid first. My boat was brown and the acid turned it white again.
As for stickers, google "seadoo decals" and you'll find numerous places that sell aftermarket decals. A few guys on here know where to get actual replicas, but I haven't had to go this route yet.