Regarding the CRO, yes just light coatings. I would avoid removing it with sandpaper as this would cause grit contamination. Consider either scraping with a knife gently or using a small amount of water and Dawn dishwashing liquid (other liquid may work but this does work) to dissolve surplus amount of CRO. Use gloves as this can get quite messy.
Unless you are quite compulsive, just leave the scratches but clean out after use. The XXC or Atoma 140 works fine for flattening, but on finer stones you can retexturize the surface with either an Atoma 1200 or DMt fine or XF. The Atomas will produce the least amount of stiction. For texturizing the smaller Atoma pieces will work fine.http://www.chefknivestogo.com/at2x312gr.html