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Since these units had no moving parts except for the gas valve the gas valve is one possible culprit. It's also possible that something has broken loose in the heat exchanger, possibly a baffle. So the first thing to do would be to pull the flue and look into the heat exchanger for loose sheet metal. I know this is going to be a challenge given where most of these heaters were installed but it's your only option short of replacing the gas valve which wouldn't be my prime suspect unless you canpinpoint te vibration to there
Is that cover you're banging right above the gas valve and manifold? I assume this unit doesn't have a fan.
The vibration has nothing to do with CO. You should have CO detectors in the house regardless. This does't look like anything to be concerned about from what I can tell from the vid and your description. If the vibration is annoying you can try wedging something against that cover so it's not so loose that it can vibrate.