What you might want to do is clean the cam cover (inside) real well and then apply some machinists bluing in the scratched areas. Replace the cover and drive around a bit then remove the cover. See if you see any new marks. I am betting that cliff is right - they were probably there before. That chain would need to deflect A LOT to hit the cover.
As far as glazing goes, I would want to minimize the time at idle. But you also need to get the darn thing tuned too. My recommendation would be to get everything fixed (clutch, brakes, etc) then go through each system step by step (Cam timing, iginition timing, etc). If you are running with SPICA a lot of those adjustments need a hot engine so you might need to live with it less than perfect. Get on the road and break it in and then worry about the fine tuning.
As far as the knock goes, did it go away with the hose clamp? If you get a persistent knock I would be very leary about going too far until you find the root cause. It might include pulling the motor and tearing it down. A pain but you would regret not doing so if you spin a bearing (as I can attest from personal experience...).
Good job getting around the block with it though - that is progress!
