Rafflesdials has a 16610 case with lug holes. I don't know how accurate it is, but at $56, it might be worth buying to find out.
https://rafflesdials.com/rolex-signed-16610-16800-vintage-style-of-40mm-stainless-steel-submariner-watch-case-with-flat-sapphire-crystal-black-click-bezel-and-20mm-lugs-have-drilled-through-holes-fit-eta-2824-or-nh35-movement-and-dial-in-28-0-29-0mm/
Yes, the crystal scratches can be polished out. A popular way to remove them is with Polywatch.
https://www.amazon.com/Polywatch-Plastic-Crystal-Polisher-Polishing/dp/B07RYPG96T/ref=asc_df_B07RYPG96T?tag=bngsmtphsnus-20&linkCode=df0&hvadid=80745502739818&hvnetw=s&hvqmt=e&hvbmt=be&hvdev=c&hvlocint=&hvlocphy=&hvtargid=pla-4584345029616316&psc=1