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Instead of leaving it as is(negative waves man) step up on the higher grits and hand sand. Now that you have rid the razor of rust and pits(I hope) go to a 600. 1000.1500,2000 grit papers(wet and dry...

You were probably seeing the marks left from applying the wheel unevenly. Instead of doing the whole blade at once you were moving the flapwheel from place to place leaving marks here and there.