I have just got my W reg 1.8 diesel focus zetec back from the garage with the same problem as mentioned, except mine started to cut out more at low revs eventually, 4th gear being the worst. Tried changing the battery, fuel filter but could't sort it.
Put it in to my friends garage, who specialise in ford work and he run the diagnostics on it.
Problem was the sensor for the accelerator was not working right, so he replaced it and its now running perfectly well again.
Dont know if this will fix your problem as i have seen a few different solutions, (breather pipes, air intakes etc), but it sounds very similiar.
The sensor cost £87 from the gargage but im sure you could find it cheaper online if you are able to fit it yourself or even just to hand into a garage.
Also had an oil leak so my oil filter was changed but dont know if this had any bearing on the problem or the eventual solution.
Hope my rambling helps somewhat.