Could be injector knock. Try cracking lines at injectors to see if noise goes away. If it does, switch that injector with another hole and see if noise follows it. I've had knocks and smoke because of fuel leaks at the return lines and also faulty or crushed heat shields. And I also have a bit of blowby--doesn't blow the cap off completely, but dances a little. Do a search on blowby and you'll find that it's really not a big deal on the whole. If you have it, really the only way to fully remedy it is to tear down the entire engine and rebuild. And like you've said, it's a hassle to disassemble and reassemble. Good luck!

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1998 E300D, 287k, barely broken in.