I decatted my passat tdi, due to low mpg's and lack of performance. It did not improve either of these by much, but the car revved more freely at the top end and the turbo produces boost earlier. This last point might make your problem worse?
I agree the cat is not necessary for passing emissions, but it is there for a reason.
I would have thought the air pressure sensors would 'tell' the ecu if the inlet is overpressurised, the boost control valve should then operate the wastegate to slow the turbo down.
In other words, the management should be capable of looking after the boost level? If you get it scanned for fault codes it might tell you if a sensor has failed?
If the intake is gunged up, it is well worthwhile clearing this out, the difference this made for me was most welcome.
Have you read all of this thread? Most juddering problems seem to be reduced by disconnecting the vehicle speed sensor ( which is next to the CV joint on the gearbox) if this works there is a certain wire which can be cut that achieves a similar end but without losing the speedo function.
The proper cure for the juddering problem seems to be stripping down and cleaning the diesel pump which looks to be a very specialised job, involving desoldering the electrical side of the pump control.