Could be something as simple as carbon buildup on the injector tips. Before digging into the hard parts run a heavy dose of diesel fuel injection cleaner like Power Service, Howe's, Lucas, etc and run the dog piss out of the truck. Don't baby it. See if the knock goes away.
If it still knocks then it might need have the injectors removed, checked and cleaned. Also at the same time check the valve lash.
It would not run if the IP was bad.
Are you guys absolutely positive that it is not just normal diesel engine noise? My old 03 was much louder at 75000 miles then it was when it was new. Knocking is usually caused by an injector issue or worst case scenario a bearing may be going bad in the bottom of the engine.......