puegeot 406 51 plate diesel misfire?

can anyone help i have a 406 diesel on a 51 plate mileage 334,000 miles serviced once every 7 weeks due to high usage has had a head reskim,complete fuel system replacement including engine fuel parts the problem is that the turbo went (still running ok but no guts) and i got a replacement fitted (by local mechanic)the correct one and now it misfires popping at all driving speeds,took car into local pug dealers plugged it into a machine said faults were as long as my arm ,they reset the computer and said don't drive over 3,000 revs this was 3 weeks ago now the misfire is back not gone over 3,000 revs and the anti pollution fault light is on what can i do can anyone help or give advice as ive spent so much money on this car