Hi Allber,
The fastest, easiest, fix would be to go chrome from Hard6.
http://www.ssmotorcycle.com/ This
could be the least expensive fix, too, depending on what your time is worth, how much of the other processes you can and want do at home, your proximity to commercial polishers / platers / powdercoaters, how much frustration you can withstand, etc...
Another option would be to purchase a pair of used wheels (+/- $300.00), prepare them in your choice of finish, install new bearings, and then do a quick swap of rotors and tires. Your bike would be down for only as long as it takes to swap out.
Any fix of your wheels is going to require removal of all of the remaining clearcoat. For the sake of completeness and safety to other pieces, off and out come the wheels / tires / rotors / valve stems / bearings and then grease removal (I did it with aerosol gunk and a self-service carwash). It's not hard, but the project gets big rather quickly.
This thread mentions using Easy-Off oven cleaner to remove the coating from rotors.
http://www.valkyrieforum.com/bbs/index.php?topic=1060.0 I don't know if it would work on the wheels, but would be cheap to try. If it doesn't work, media blasting would both remove the clearcoat and leave a surface easier to polish. Post-polish, you can maintain with polish and/or wax sealers, or you can go back with clearcoat. Kinda like Honda.
If you go powdercoat, they will probably want to sandblast to provide a rougher surface for powder to grab onto. The guys I used, Custom Powdercoating in Dallas (GM John is an old MC friend), did not recommend clear powdercoat over polished aluminum.
When I got my 2000 in 2007, the uncoated wheels had been allowed to corrode and pit slightly. They weren't terrible, but they were by far the worst cosmetics on my bike. With the wheels still on the bike, I tried the Mother's Powerball + polish method, but that was not aggressive enough, was taking forever, and I couldn't reach the entire wheel (it did great on the rotors, though). I switched to sand paper and got better results, but couldn't reach the entire wheel. Out of frustration with the polishing process and the future need - even if minimal - to maintenance-polish aluminum or chrome, I chose a 2-step Sparkle Silver + Clear powdercoat. They look like freshly sandblasted aluminum with a bit of sparkle in the sunlight and thick clear on top. I sacrificed sheen for really easy to clean. That wasn't necessary, but they are a little different.
Come to think of it, they are almost the color of road film.

That must explain the tan Explorer in the driveway and why
dirt-colored tan carpet is so popular...
Hope this helps,
DFG
For additional info, this thread about aftermarket wheels was on the Tech Board last month.
http://www.valkyrieforum.com/bbs/index.php/topic,2486.0.htmlHere are some videos about polishing.