The stock wheels on my 2009 SG are not too bad, but have stains after 4 years on the highways. I did some research over the winter and found a recommended process on the Meguiar's website for stained HD stock wheels. I will try this process when I get my bike out of winter storage. This will take some time and elbow grease and willing to give this a one time try.

Meguiar's recommended three step process for stained HD stock wheels:
(1) Clean wheels with Hot Rims Aluminum Wheel Cleaner.
(2) Apply the Medium Cut Metal Polish.
(3) Apply the Finish Cut Metal Polish.

 

A lot of great feedback here. Clearly have options.

Sarge thank you sir for this link. It's worth a ride over to see him. Maybe he could do my wheels and forks. His work looks chrome! I'd like to understand what he does and how it holds up.

 

I just picked up a set of Streetglide wheels of e-bay and will switch over when new tires are put on..

 

Quite often it is chemical burn from using harsh cleaning products left on too long before washing off - the ops bike looks more like rust

00 grade wire wool and autosol (for bad stuff like the picture) or belgom alu for less damage - go with the 'grain' of the aluminium.

Once back to a decent finish use acf50 as a proofer against future rusting

 

the 2 different photos of different wheels shows 2 different problems.
The OP has mildew, this is caused my high humidity. It is a fungus.
The only sure way of removing it is to use sand paper. The fungus gets into the metal not just on it. I do a lot of wheels for folks, polishing. I have seen a lot of it. After sanding you can polish.
The other is salt burn, it also gets in the metal. The solution is the same but may be harder to remove.
Both cases could have been prevented by cleaning more often.
you may get some of it out with steel wool but not all of it.
On my none chrome wheels I use bleach white to clean them, The bleach will kill the fungus but will not remove the stains once it starts to grow.
I am a horticulturist. This is how I recognized it the first time it was shown to me. Had to do some research, to confirm my thoughts.
dd

 

My 10 Ultra did the same thing.I asked a tech at the local dealer and he showed me what to use,it's not a Harley product but this dealer sells it.I can't remember the name but when I get home tonite I'll get it and pm you.It's a little work and slow but it worked on mine,been 2 years now.

 

If you have them off the bike, and have a blue beacon truck wash in your area. Take them there and ask if they will brighten them up for you. The acid they use will clean almost anything off aluminum.

 

I have a 2011 FLTRX & use Simichrome Polish. My wheels are NOT clear coated. You'll find out as soon as you start to polish. The rag will turn black. Mine is from riding along the coast(salt). Good luck.

 

Wow what did you run through that stained your mags like that?

 

powdercoat them!