With my 2002 5.3L, I am currently experiencing similar knocking coming from the underside and where the engine and trans come together. It subsides once warm. I also have a bad rattle above 3500 rpm's
Also, engine codes 300 (random misfire) and 507 are coming up on the code reader.
P0507 is Idle air control. Code is thrown when the PCM detects engine idle speed that is faster than the idle RPM should be. Could be unmetered air. (vacuum leak) from PCV, EGR, or anywhere, even intake manifold gasket... faulty MAF, IAC. Regardless, even with P0300 I don't see how that would cause a knock, any of it
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