Diesel Doctor

Can anyone tell me what to look for? The truck has almost 200,000 miles on it, on a cold start after several hours of sitting it starts and stalls, it will stay running if i give a bit of throttle, runs rough like its misfiring smokes black. Once it warms up a bit still runs rough, smokes when accelerating, mainly grayish color sometimes black, lacks power as well almost feels like the transmission is slipping. There is no check engine light on, still ran it by a friend who scaned it with one of those fancy scanners he said there is no codes in the computer. I did replace the fuel filter, it was very dirty and a lot of black goo in the botom of it. it did stall out at times before i changed the filter, seems to run a little better and doesn't stall out anymore.