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It's possible it's a fuel problem but it doesn't explain the knocking sound.
Any fuel leaks? Good fuel filter? It's possible it's a bad tandem pump. On the driver's side end of the head there's a dual fuel and vacuum pump. Normal fuel economy? No other error codes? There's an electric fuel pump in the fuel tank. It's possible it's cutting out or clogged resulting in no fuel.
The other injection pumps are the injectors themselves. If there's a wiring problem to the head (look at driver's side round plug), it's possible it could result in fuel cut.
Good engine compression? I'm not sure if the knocking sound at idle is a bad camshaft but have you inspected the cam? http://www.myturbodiesel.com/1000q/multi/camshaft-inspection-replace-VW-TDI.htm I don't think this would be silenced by stepping on the clutch though.
Any fuel leaks? Good fuel filter? It's possible it's a bad tandem pump. On the driver's side end of the head there's a dual fuel and vacuum pump. Normal fuel economy? No other error codes? There's an electric fuel pump in the fuel tank. It's possible it's cutting out or clogged resulting in no fuel.
The other injection pumps are the injectors themselves. If there's a wiring problem to the head (look at driver's side round plug), it's possible it could result in fuel cut.
Good engine compression? I'm not sure if the knocking sound at idle is a bad camshaft but have you inspected the cam? http://www.myturbodiesel.com/1000q/multi/camshaft-inspection-replace-VW-TDI.htm I don't think this would be silenced by stepping on the clutch though.