I'm still going by you saying for now you gotta make this engine live. If it were mine and it was in spec, I'd run it. (The scratched cap) Definitely make sure whatever caused it is cleaned out of the oil passages. Make sure the cam surfaces aren't causing it and they are in spec. Basically...
I would follow the FSM if you have one. I have zero experience working on a 3.0 but generally speaking on engines, I'd make sure you have a good flat deck surface and head surface. Hopefully the cylinders look ok. My experience is valves "typically" get tighter as the seats and or valve faces...
A tight valve that doesn't close all the way will give you low compression. A loose valve will give you noise or more noise than a properly set one anyway.
If they let it get too tight and burned a valve, then tried to adjust after the fact can give you lower compression.
A leak down test...