I've got a 98 SPX with the exact same yellow hood. My advice is to not even bother trying to get the stains off the cover; It'd be an impossible task. I tried to clean mine last year and it left the cover with a perpetually sticky feel and I still couldn't get rid of the black mildew spots.
Also, you're right that you don't want to try and paint that rubber. I tried that approach with a vinyl spray paint and it turned out real nice...until it got wet. The paint lost all adhesion at that point and flaked away. The most promising fix is to use a product called PlastDip. It comes in a brush on formula and a spray on formula. It basically puts down a new layer of rubber. I used the spray version on my cover and it turned out really nice. It comes in a variety of colors, including yellow, and is about $6 to $7 a can at Home Depot and Lowes (in the spray paint section). You may have to order yellow if it's not stocked by either store. I used black to avoid any further, visible, mildew spotting.
Well, the cover isn't yellow anymore; but neither is it visibly spotted or sticky.:hurray:
If you go this route then there are a few rules to follow:
1. Don't remove the steering cover, mask around the cover and use a tarp or newspapers to cover the whole seadoo to prevent overspray.
2. Make sure the cover is clean and free of grease.
3. Use thin coats while spraying; this prevents dripping and thick coats do NOT adhere well.
4. Go with 3 or more thin coats with a couple hours between applications.
5. Do this in your garage unless you want pollen to be a permanent part of your seadoo.
You can use either the brush on stuff or the spray; I used the spray because it was easier to work with and I wouldn't end up with brush strokes all over the cowling.
I hope this is of some use to you.
Props to jbake728 for the original idea.
original thread
http://www.seadooforum.com/showthread.php?p=57628#post57628