The aluminum fork legs, triple tree yokes, engine side covers and wheel hubs are aluminum that has a surface what was brushed with a sanding drum at the factory - then clear coated.  The surface is not completey polished smooth under the clear coat - but has a series of directional scratches that does reflect light.

The clear coat is not excpeptionally durable, and when it breaks down it allows water to get to the aluminum and corrodes it.

Making the surface look line new is tough.  The clear coat and bare surfaces need to be the same...either coated or not.  The clear coat can be stripped with paint stipper - but then you need to either paint the surface to get it to look good, or you can lightly sand it and buff it and either clear coat it again - or if you don't let it sit out and only ride in fair weather you can leave it bare and polish it regularly.

Some of the people on this site have used Scotch Brite pads to just scratch the corrosion and get the bare aluminum to match the surface under the clear coat.

I had some corrosion on my engine cases.  I took them off, stripped the clear coat off, and then machined buffed them.  They look good - but the aluminum is very soft and scratches very easily.

Wow! For an 05 that is not just neglect, but abuse of a motorcycle  

I don't have experience in sanding/buffing the aluminum on these bikes so I will leave the advice to the others, but welcome and hope you enjoy the ride  

p.s. You probably want to check/replace those tires...even though they only have 2300 miles on them they are probably in need of replacment

Thanks for the help! I may wait until the off-season to do the aluminum and just keep focusing on the chrome for now.... as ugly as the bike looks from this damage, it runs perfectly, bought it for a steal, and love working on it

There's a point where deterioration, becomes art,...
the Japanese call it "Wabi Sabi"...
I think I like it...
...

3M green pads on a palm sized jitterbug sander stripped the junk off my cases. Keep a spray bottle of water handy, wet the pads & cases some. YOull learn the optimal amount, about the time youre done,
Rattle can clear works fine,

A little jitterbug will create a texture that doesnt have straight lines & knock the crud off real quick., It will create a matte finish that looks really close to stock after the clear. IF ya use the water.

All by hand, but I think I'll go buy a jitterbug to do the rest.

Thanks to the feedback, I just use some paint stripper to take off the gloss, then a 3M pad to knock off as much crud as I could (with or without water, I didn't do as much of the job as I was hoping for). I tried a wire brush at first, but it made too many scratches for my liking. Then used some waterproof 400 grit sandpaper with a little water (by far the longest part of the job), then 800 grit sandpaper, followed by #0000 steel wool, before finally some aluminum turtle wax.

Once I get everything to at least a non-embarrassing state, I'll probably go back and try to get it all show-room shiny.