Diesel Bombers - 6.0 running rough all sudden

I have a 6.0 2006 with a egr delete engine oil cooler and new head studs done 8 months ago. Ran great until recently today got gutless and was running rough all sudden after it ran fine this morning. Weird it was only parked for 3 hours started it back up which btw this is a daily driver truck and went to proceed to town to get some milk. Well it knocked and sputtrred and golly acted like it wasn't getting fuel. It was on 1/8 of a tank so I went to orielys and grabbed some diesel clearner and followedthr directions then fueled up. Then took a drive to use a 1/4 of a tank of it too on hey. It got worse and was blowing some nasty smelling black smoke ehen it did finally accelerate. It wouldn't shake and stumble much doing 70mph but in lower speeds and waiting at red lights it died once. You could tell when it got fuel bc it would smoke like non other and have power. Im not rich and was wondering what would cause this and please put in simple terms. Btw ive worked rpund diesel motors and by far not a dumb gal ive rough necked several years and know the basics to mechanic. Do yall think its a fuel filter issue is there an water separator? Top fuel filter looks great got to dark and storming to check the bottom tonight. It starts right up just runs like crap and smokes worse than my straight piped 7.3. Im a country gal but really dont have a mosquitoe problem lol. Help