I would check the air filters on the engine. 10,000 miles ago I bought a used 2007 R320 CDI from a dealer. Recently, I decided to change the air filters myself. It took me two hours and it looked like the air filters had never been changed in the first 40,000 since it was built in the factory. I have owned more than 30 cars in my life and I have never seen air filters so plugged. It was amazing the car even ran.
I seriously doubt that the dealer would replace the air filters unless you asked, because they are so difficult to replace.
I would also change the fuel filter to make sure the engine was getting adequate fuel.
I would also check the wires in the engine compartment to make sure that the insulation was not falling off. I had that problem with a diesel Volvo in California because the smog made the insulation fall off like powder and all of the wiring harness in the engine compartment had to be replaced when my Volvo diesel only had 270,000 mile (just a baby).
Good luck! Remember diesel run well if they have adequate compression, unplugged injectors, adequate fuel and adequate air.