I would suggest a talk with Mrieck, he is the big cylinder head guy
The divot for the valve cover is odd, did you have the head sent out or did you do it yourself? It is pretty big in size, not just a tool mar
As for the chamber marks as long as sealing surfaces and the valve seats aren't chewed up it is "ok". "Ok" tho is a matter of opinion and everybody's is different. I would polish down any raised surfaces to not have hot spots and then sit the valves in place and test them with alcohol to see if they seal.