I bought a 6.9 Idi starts really well in cold and warm it has an 88 injection pump doesn't smoke at idle but if your in second gear for more then a few seconds it will smoke and spit and sputter but under acceleration it feels really strong. Will do it in 4th gear too I've noticed. Could it be air in the system or could it be the injection pump isn't correct?
When I bought my 1987 6.9 two years ago it would temporarily idle rough in overdrive, seemed to have more power too. I ended up replacing the injection pump, injectors, and return lines. The injectors on mine were leaking and I presumed under extra load they were dripping and partially igniting. I'd replace the injectors, and return lines. If you have the clams then you can buy or have an injector pump rebuilt.
If you want to hold off on the pump then depending on the smoke (white=retarded timing) (black=proper or advanced timing) then you can advance the pump, SLIGHTLY, (many videos on YouTube). I'd only advance a dime's width from the pump center mark, you don't want it to sound ridiculously advanced (very loud/knocky/chattery) and you don't want too retarded.