So....... Update. In tearing apart the old motor, turns out, there were some poorly adjusted rocker arms causing the noise up top. The motor had one 062 head and one 906 head on it. AND...... There was a piece of rag shoved down in one of the coolant passages on the half ton head.
When I put a light up to each exhaust port on the HD head, I could see light around every seat. Talk about losing compression. No wonder the motor was weak, idled rough, and had a hard time starting.
I'm also not so sure it's an L31 HD bottom end. I'm pulling the oil pan tomorrow morning to be sure, but I'm betting the "new" motor the previous owner had put in was a piece milled piece of junk.
No matter now. It's all done right, and it runs like a champ.