2004 Touareg 2.5 TDi R5 missing / booming noise from engine

This noise is coming from the engine bay, particularly by the air filter. The noise can be cancelled by moving the valve / flap as shown, but there is something wrong in the engine. Suspect is injector, valve, piston or something else, but without a plug in diagnostic, I’m open to suggestions. Update: The problem was a worn camshaft and followers. I replaced them with the engine in the car. It took around 5 hours, with the hardest part getting to and removing the tandem diesel and pneumatic pump. The parts I used were plus I bought the special tools, I hope this helps someone.