Knock isn't unusual on a cold engine - ramp up the idle speed and let the pre-chambers warm up before driving, at least until the temperature gauge starts to move.
Knock on a warm engine: idle speed too low, leaky injectors, bad timing. Remember a diesel sounds like a diesel.
I'd do the fuel first. If you can do the brake lines then you can do the rubber fuel lines. Drain and biocide the tank while you're at it. Have spare fuel filters ready. Won't touch the diesel purge vs. ATF controversy after reading the archives (I'll follow the combined 90 yrs experience of two injector pump shops local to me). I also have a water separator and use Power Service DieselKleen continuously.
Then I'd double check the valve adjustment and measure the timing chain stretch while I'm in there.
I'd then set idle speed, after I've checked the governor vacuum system for leaks and operation, and making sure all the linkages are cleaned and lubed. I borrow an adjustable strobe light from work, but there are other alternatives out there.
Also: if an oil bath oil cleaner then check the oil and clean the filter, which is the basket in the housing, if the oil is dirty. Gas takes the paint off so I use a tub of soapy water and slosh the filter in it, slosh in clean water until no soap comes out, let dry overnight, then soak in oil before reinstalling. I use the cheapest 30W C-rated oil I can find for the summer months, 5-whatever C-rated oil for winter (the 5-whatever was for a 1970 pickup that I wish I still had). The cleaning drill is a good lesson to keep the oil in the housing clean.
Drive it for another 500-1000 mi and check results. For me clean fuel is the first trick to a diesel. Then patience for the system to clean itself.
THEN I'd look into adjusting timing and having injectors tested. The Bosch web site is
www.boschusa.com. Click on auto parts, then diesel service (I think) to find shops where you live.
Good luck and let us know in 500-1000 mi.