Sounds like your problem is with your DPF (diesel particle filter) The juddering and loss of power is the system trying to regenerate itself.
There have been lots of issues with theses filters and VW have done a quick fix by uploading revised software at service time. The problem with this is it is losing around 15bhp in the process. They hoped that most people would not notice, but word has got out.
There are companys that will fit a Milltek DPF replacement pipe and remap the ECU to take out the regeneration process altogether. This mod will not only cure the problem, but will see you with anything between 220-240bhp with better fuel economy. Also at around £6-700, it is cheaper than replacing the factory DPF with a new one.
JBS at Chesterfield seem to be on the ball, so it might be worth giving them a call.