What is it like at higher revs ? does it smooth out completely or does the juddering stop to be replaced by an odd feel esp when cruising at high revs (3k onwards and a sort of lurching feel) like it is hesitant.
Does it start ok from cold and then drive ok for a few minutes until it starts to get warm and then the problem start to surface ?.
Does this problem come and go in it's severity ?,drives nice sometimes and then behaves badly and then back to bad and various states in between ?.
Get the codes read first and if nothing shows then plug a clear pipe in place to replace the one from number one injector that runs back to the return on the top of the injector pump.
Use a long length of pipe so you can leave a loop in it so it is then the highest point in the fuel system.
Drive it around for a while and then check the pipe for air bubbles whilst the engine is running.
If you see air in the pipe then the next thing to suspect air is getting in to the fuel system.Now if it is not in the clear pipe to the pump then it is getting in through the leak off pipes or the worst case scenario the injector pump front shaft seal.
I had this on my tds and spent around a month fiddling around changing pipes and scratching my head.
The give away was that my sump oil level went up by a litre,fuel leaking past the seal entered the sump when air was not getting sucked in to the pump causing the rough running.
I changed the engine oil and filled to 3/4 on the dipstick and then checked it 100 miles later and it had risen,so I had to remove the pump to fit a seal that takes a few minutes to fit and costs around a fiver.
This is the worst case though and if you have the correct tools it only takes around 3 hours to do the job,but if all other checks draw a blank then this is what it will be.
As with yours mine would smooth out when throttled hard,mine still drove well when constant acceleration but did not want to cruise smoothly at all.As with the cold starts mentioned above it was nice when first started,so nice I would think the problem had gone away,but as it warmed up it would appear again.
I think the lift pump running at cold start expelled all the air out of the pump and stopped it drawing any in,when the engine is part warm the ecu runs the relay and turns it off and on as dictated to it by a pressure sensor in the fuel filter,I think as soon as the ecu switched lift pump off for a while then the air got in and the misbehaving starts.