Are you sure it's not just slowdown shudder?
There's a couple of things you can consider based on what I've seen in the family garage.
Injector problems, or a compression issue, vagcom should show this/rule it out.
The crank case sensor, could be faulty or simply need removed and cleaned and re mounted correctly again.
Personally I think it might be, throttle related, à faulty throttle sensor can cause momentary low voltage signals to the ecu, confusing it. A could way to rule this out/prove it is see if you can reliably replicate the issue, then try replicate it while on cruise control, so the throttle pedal isn't controlling the signal.
The egr is operated by a vacum line in the fl 1.9tdi isn't it? If so check it isn't leaking anywhere and the ehr is defiantly closing and shutting properly.
I would try the cruise control test first, if no luck best think to do is to make a vagcom request and get some logging done, then post the results here and I'm sure one of the talented members here will steering you closer to the answer
