Brendan--Are you talking about the actual inclusions in the metal? If so, my honest suggestion is to bring the metal around it to a glorious luster and don't try to go after the inclusions. I've made the mistake of trying to get rid of them, and ended up messing up the grind lines of the knife because of removing so much metal. Just leave them be, and keep the rough-forged look. Honestly, it's kind of neat, and gives you a three-finish effect, with the hard edge/temper line, satin main grind, and slightly rough flats. That's what I did on my second attempt, and I'm much happier with the result.
If you're just talking about the non-included scratches, then get some 180 grit 3M paper and a wooden sanding block, press hard and go to town. Once your finish is even, move up to 320, do the same, and go as high as you want. I like getting into triple digits with sandpaper, and then polishing rouge on leather, but it does take some time.
Good luck!
Warren