David, those small marks on the shaft can be further reduced by judicious use of a file, making your strokes around the periphery, not along the shaft. Just remove the part that is raised up above the original level, don't reduce the diameter of the shaft. Once the raised up part is gone, the marks will be quite inconspicuous. However it would be wise to do this after you put it back together, since you may make new marks when you re-tighten that nut.
