People often conflate "clean" with "no wear". Cleanliness and wear are two very different issues. Since the purpose of pulling the valve covers was to check valve clearances, I'm curious how the clearances tested out? Were they still in spec, or did many of the valve shims need to be changed out? If so, which ones, intake or exhaust? The exhaust valves and valve seats are more prone to wear than the intake valves are.
Oddly enough though, there are two different wear mechanisms which cause the valve clearances to change on an overhead cam engine. If the valves and/or valve seats wear then the clearance tends to be reduced. If, on the other hand, the camshaft wears then the clearances will increase. If both are wearing at similar rates then the clearances will remain constant, but the valves will open slightly less than they did when new.
Oddly enough though, there are two different wear mechanisms which cause the valve clearances to change on an overhead cam engine. If the valves and/or valve seats wear then the clearance tends to be reduced. If, on the other hand, the camshaft wears then the clearances will increase. If both are wearing at similar rates then the clearances will remain constant, but the valves will open slightly less than they did when new.