Possible injector blockage or contamination? Was diagnosed by Ford as causing jerky running of my old Focus 1.8TDCi. You could try running some injector cleaner through with the odd high-revs blast through the gears. I would have thought though that a blocked injector would affect running at all speeds and not just one particular speed/gear.
A dirty / sticky EGR valve is another possible cause of hesitant running. You could take a look inside and check how much soot/oil build-up there is and whether or not the valve opens and closes smoothly.
What is the engine speed at 35/40mph in 4th gear? Could it be the engine is labouring off-boost and perhaps the dual-mass flywheel does not like being asked to transmit torque at low revs. The drivetrain in my Seat Leon TDI vibrates and resonates when asked to pull from <2000rpm in high gears and the flywheel can vibrate quite badly. If the DMF is worn it could start juddering which could be mistake for engine symptoms.
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