First off, I have no experience with CF boards, but I would treat it as though it were wood and go back to 600 or maybe 400 if that will take out the existing scratches. Then work it up through 1500 paper and move into the finer Micromesh grits until you reach fingerboard Nirvana.
Use a longish cork-backed sanding board to keep it straight and bump free.
Obviously use long, even strokes to maintain the shape of the board and rember that its not how hard you push, its how many times!
Jake