mondeo zetec tdci

can someone help, 2002 52 plate Mondeo diesel zetec , The vehicle just stopped, the first garage put a new diesel pump on then sent it to ford
specialist to reprogramme. The ford specialist bill says no 3 injector faulty, replaced and all injectors recallibrated. Ford sent out latest software and they installed it. They said it was ready to pick up and i paid but it was running on 3 cylinders, knocking bad at low and idle , blowing smoke out at start. Car runs well under acceleration. First garage then put a new dual mass fly wheel on. Its still knocking and smoking but runs well on the road under acceleration. Any suggestions please
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