All valves out of the box are not concentric to the stem. Maybe they forgot to grind them. Some of us are anal enough to even mark the valve stem where it comes out of the valve guide inside the bowl and index that when you chuck the valve into the valve grinder. Anyway, I always check a couple intakes and exhaust valves in each head by hand lapping the valves to check seal and seat width. Anything bad shows up real quick and easy to see.
As for the cylinder scratches, maybe it is the rings? Who gapped them, and what gap? Look for shiney spots on the ends where they may have butted at temperature.