2008 Toyota Van A loud thudding sound

I Own a Toyota hi-ace 2008 with a 3L turbo engine. Recently when I pumped diesel from the local filling station where I pump regularly apparently the diesel stock at the filling station was running low and a high level of residue had entered the car. Over time like about 5 minutes onwards gradually the car developed a jerky rough drive that eventually after about 50km turned into a very jerky drive with a loud thudding noise. When towed to my local garage the engine diagnostic test reported as the vehicle to be fine but the engine has a loud noise. The garage asked me to take it Toyota but I haven't decided yet. Apparently one more thing they stated was the injector pump pressure was also very low. When diesel was taken out from the filter it was with high residue a blackish colour and dirt in it.