What were the results with the clear lines and the other fuel system checks above before you get into any of this stuff.
Is it one cylinder?
Possible Injector?
With engine idling crack one injector at a time and identify which is the culprit. After you ID which one, kill truck and swap that injector with another one and see if the knock follows the injector, or stays at the cylinder. If it moved with the injector- that's the not happy one. If that injector is coked up, try soaking it in carb cleaner and use a soft tooth brush to clean away deposits. DO NOT scrape at the tip of the nozzle, the pintle is a needle tip on the end that is easily ruined.
If the noise does not follow the injector it is something in that cylinder. Do compression test and cylinder leakdown test. Pull valve cover look for rocker button, free play in arm being worn,bent push rod,collapsed lifter.