Jon,
First thing you gotta know is there are about 14 coats of paint on the fenders and tanks. Really! I would recommend NOT doing anything more than just cleaning and filling the scratch with the paint. I would imagine as soon as you start to sand or anything, you will end up with a large discolored area and end up repainting the entire fender.
I had a few little scratches on my fender, and just used the touch-up paint and it looks fine. You can't see it unless you know where to look. I have a spare tank that Jaymo gave me with a big chip in it and I was amazed at how many coats of paint there are on the thing. Some colors even use a variety of colors and blend as they coat the parts to get the final color. I think that is why you cannot get the Capsian blue - it's not just one color.
