I've rebuilt my fair share of engines and I've seen plenty of rear seal grooves on the cranks. The new rear main seal will be soft and flexible enough to seal it, even with the groove (was it leaking out before disassembly? was the old seal hardened?). I wouldn't try to use epoxy or anything on it though. If you really want to repair it, look for an actual rear main seal repair kit (many companies make them, I've used Pioneer ones but I could only find microsleeve in a quick google search of "Rear main seal repair sleeve"). It'll have a stainless steel cup that gets pressed over the original seal surface. It's very thin and can be broken or distorted easily so you may want to have a machine shop install it for you.
As for cleaning, most machine shops will hot-tank (cast iron) or cold tank (aluminum) components for you for a cheap fee then just use dish soap and water with bottle brushes to do the final cleaning before assembly (compressed air to dry and blow out bolt holes and passages then wd-40 on any machined surfaces).