No the 2.5L motor in question is a single-cam, 2-valve, 5-cylinder design. The OM606 video you linked to is a different engine and that one sounds like it has a bad belt tensioner shock.

pdrayton, I'd bet it's the injector. Sometimes they need some time to settle in or clean out the combustion chambers if the previous injectors were spraying poorly. You can try cracking each injector line to see if the noise goes away. If it does, then it's a combustion knock instead of a mechanical one. Or you can try running the engine on Diesel Purge which has extremely high cetane and it will at least temporarily quiet down any combustion knocks.

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2004 VW Jetta TDI (manual)

Past MB's: '96 E300D, '83 240D, '82 300D, '87 300D, '87 420SEL