The price sounds good to me. The one thing I would be concerned about is how it was broken in. Normally XB12x's aren't owned buy the young and careless type, but the fact that its used always makes me wounder how the previous owner treated it. See if the dealer will throw in some kind of extended warranty.
Yes other buells shake at low RPM too.
The discoloring shouldn't be that bad if it only has 600 miles, but it should be a bit discolored. If you are concerned about it, you could always have it ceramic coated.
Start with the breather hose re-route mod.