Holden Captiva 2009: Engine dying

I've just replaced the diesel motor in my 2009 Holden Captiva, due to the back up of carbon which blew the motor and I do a lot of long distance driving, now while accelerating the engine will suddenly die around 2000 rpm then go again but blowing black and blue smoke. Have had the computer totally gone over and tested also same with engine but no luck. Can you shed any light on this?