Chrome is a plating. If "little bumps" are appearing, then the plating has corrosion underneieth and is failing. I've used #0000 sttel wool with MOther's Mag Polish with good results, but you need to keep it dry and waxed to stay nice.
Engine "water spots": The engine is powdercoated silver, and polished parts like the rockerboxes and side covers are polished alumunum, powdercoated as well. The "water spots" you see are blemeshes in the clear coating. You can use a fine polish to get most of those off. In extreme cases, you have to remove the clearcoating. Probably not the case with a 2006.
Polsihes that I've used with good results:
*Neverdull
*Semichrome
*Mother's Mag Polish
I also found this new stuff on the internet called "Long Haul" that's sold at truck stops. It's a liquid and works well too.
The only true way to get rid of bad corrosion is to sand/strip off the powdercoating, then polish the aluminum. It's a long painful process, but the results are worth it.
My front forks were all skanky. Bike's previous owner let it sit outside, for lack of a garage.
Forks were stripped with a 3M grinding pad (red), then gray, then 400 wet paper all the way to 2000 wet, using WD40 as a cutting oil. Then polished. You don't have to take the forks off to do this, (although I did, since I was rebuilding them enyway) but taking the front wheel/fender off makes it a lot easier.
"Aircraft" stripper works well too and saves a lot of elbow grease, but you have to be really careful that it doesn't get on anything else.
Original forks (and bike for that matter) You can see how bad the forks are, and the cam cone is almost a white, corroded hunk of aluminum. It had to be replaced.:
And now:

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