05 6oh issues what is the cause?

Since the last reflash in April my truck has done a few poor things. When I pull up to a light or exit the highway and try to take off again. It hesitates and can blow black smoke then spool up and run normal again. Then about 4K miles later at 40K it started jerking and bucking a little in gear at idle and cruising up to part throttle. I have to stand on the brake at a light now as it will creep as it surges. I thought I got rear ended the first time it happened. I shot a video of it but don't know how to post. The idle surges up and down about 50-75rpm worth kind of like a gas motor missing on one cylinder. The boost and EGT remain constant while it is hiccuping. Now it does both stumble, blow smoke and surge.. Thanks for the help guys!