I have a 2005 Duramax and 2 months ago had to replace head gaskets...now I'm having more issues.

A week ago we took the truck on a trip and before leaving we changed the oil and put new fuel and air filters on it. The truck was fine for the whole 1,000 mile trip but after getting back I ran it low enough for the "low fuel" light to come on and have been having issues since. I put a small amount of fuel in it during my lunch hour, went home to eat, let it sit for about 45 minutes and then left to go back to work. On my way back to work I came to a stop sign and when I went to take off the truck started chugging and lurching forward at about 5 mph, then took off and blew a cloud of black smoke. It didn't do that again for a week until last night. It seemed like a fuel filter issue so this morning I went to get a fuel filter and it kept cutting out so I left it and took another vehicle to get the filter.
Got back...put the new filter in...and of course I cracked the separator on the bottom of the filter so I had to go get one of those. After getting the fuel filter and new separator put in the truck was hard to get started. Once it was started it was idling rough and blowing a little bit of gray smoke. (The "water in fuel" light flashed each time I started the truck in between priming the fuel.) When I got on the accelerator it turned to black smoke and quit idling rough. After a while I tried driving it around the block but it was still chugging and driving rough so I parked it and got some fuel additive (Iso-Heet and Power Surge). Can someone help me? I've had trucks with injectors going out and this didn't seem to be how they acted. I'm hoping it's just a case of bad fuel...

 

It could be some bad fuel,or it could have alot of air in the fuel system.