remove the parts
mask surrounding area about an inch around the damaged area, unless you have several pits or scratches, if so then sand entire area starting with 400 then 600 grit wet sand paper, until you hit paint. use an air brush or touch up gun, spray color matched paint. wait a couple of hrs, then clear coat using air brush or touch up/detail gun.
if pits or scratches are deep I suggest filling it with a good 2 part primer. if its a deep scratch I usually fill the scratch or pit by using a brush kinda like using bondo. they're pretty much the same thing, except bondo uses more plaster which makes it thicker. when filling the scratches, dab the scrathc with a small paint brush or match stick filled with primer. let it dry then do it again. Do this a few times until the primer is a little higher then the paint. then gently sand the lump down till it is even with the surface.
then spot paint with air brush or detail gun. wait a couple of hrs ( you usually have up to 24 hrs to clear after paint is applied). then wet sand area starting with 1000 grit wet sand then, 1500, 1800, and 2000 then polish using a high quality rubbing compound. I find polishing the entire bike after with automotive headlight and glass polish works well. Polishing the entire bike will help blend the new paint.
On the other hand aftermarket fairings are pretty cheap and if you do the prep work sanding your fuel tank. A body shop will charge about 200 bills for a repaint. Probably save you alot of hassle!