Looks like spring parts took a free ride to the top and bounced all around getting under the decomp, I'd try the valve cover on and torque the bolt, if it holds don't worry about the scrapes..doesn't really matter. Pretty sure 104 in lbs is way too much, 55 in lbs for the valve cover bolts that go into the cam caps and 69 in lbs for the other two.
When you split the cases you want to pay special attention to the needle bearings on the ends of the shafts, you can see one in the pic I posted. When debris goes between the gears it will spread the shafts apart and the needle bearing is the weak link. Fiddle around with them, spin, wiggle..if any needles fall out they're bad. I would be replacing every bearing in the entire engine plus the oil pump, there are a couple of bearings in blind holes that are hard to get out, a welder helps or take it to a machine/engine shop.