unfortunately it is a trait of the tdi's and it can be sorted to an extent but its always there...I had the feeling like it was miss firing but when I put the bluefin map onto it it went away but I still get the odd little shake now and again.
The EGR valve at the front of the engine is one of the culprits it has a flap inside and after time if not cleaned will clog up and cause starting and running problems, also the threads in the manifold at the top of the EGR valve are very fragile and once threaded are a pain cos the EGR will be the weak spot for pressure leaks.
The only other thing ive noticed with these engines is the lower coolant pipe can break down due to oil and road grime and then the coolant loss starts.
Darren