Need help with this please...misfire on acceleration and more

Hi everyone. I've run into a problem and I need your help. Hopefully someone will know the answer to my problem. I'll try explain it the best I can but feel free to ask questions for more information.
My truck:
08 Western Star
Detroit Series 60
Full delete
Motor was rebuilt about 3 years ago (125,000 miles or so)
New Turbo after delete because jake wouldn't work with the old one.
New clutch and rebuilt transmission 2 years ago

This problem started about 2 years ago but only happened once. I accelerated quickly up onto a highway and the engine stumbled...like it wanted to stall. But it cleared up right away...puffed some smoke and it didn't happen again. So i never thought much of it.
About a year and a half later...it started happening more regular but was still very intermittent.

PRESENT (last 6 months to now):
It started doing this quite often now. And seems to be worse when I'm loaded and going up the gears. Basically, I start rolling from a light and it stumbles and farts out some white ish - brown smoke and the evens out. Then, I grab another gear and it does it again. And so on.
It doesn't do this stumble and fart everytime...about 60-70% of the time I'd say. Depends how hard i get into the throttle.

What it HAS started doing pretty much all the time now...when I'm loaded and going up an incline...I need to downshift because if it drops to 1200-1300RPM...it will start vibrating the cab of the truck. When it started doing this...I crawled under and inspected the driveline and it was good. Also, when I roll the window down...I can hear a bit of a "sputtering" from the exhaust.

It doesn't throw a check engine light...but i got my local shop to check it with the computer anyway (because I've never seen a check engine light since the ECM was reprogrammed after the delete).
They did find a code and changed the injector harness and inspected injectors.
That didn't help and that's when I noticed the vibration on my next trip out. So i took it back. He changed the pressure side filter and checked tank Vents.
I ran about 2200 miles the next week and it was a little smoother but still had the cough and the farting smoke on acceleration.
This trip out...its all back to bad.
I took it into a TA PETRO to get a light wiring problem fixed and figured I'd have them change the pressure filter again....and the Davco.
There was a young new guy doing it but there was an older guy teaching him. From talking with him...he seemed to know his stuff.
I told him my Davco is only half way up but might as well change it. He takes a look and says "It's black so it's plugged". Drains the fuel from the housing and it's dirty. Little black sand - like pieces and even some metal looking filings. Then pulled the filter and looked in the housing and there was small clumps of black sludge in there. Looked into my drivers fuel tank (which was less than a 1/4) and shines his flashlight. The inside of the tank isn't shiny but more of a tarnish. And the fuel looks dirty and grey. As well as black Sandy looking stuff in the bottom.
He figures it's my fuel hoses are rotting.
We replace the filters and it idles a bit better but you could see the filter (slowly) discoloring darker.
Since then, I've run about 1000 miles and it's terrible again. Probably after 400...I noticed the vibration is bad again and the sputtering and miss on acceleration (which never went away but was a bit better) is back to terrible.

I figured I'd ask in here for advice. I've spent about 2500 bucks already trying to troubleshoot this and it seems worse than ever.

Thanks for reading this long post. Any help is appreciated.

 

I bought some stuff today to put in for algae but I need to get a filter wrench (for the spin on filter) before I put it in...so I can change it if it plugs off. Hopefully the Davco would catch most of it and hopefully I'd catch it before it ran the engine out of fuel because this thing is a pain in the ### to prime when it runs out of fuel.
I had a young lady mechanic change the filter about a month and half ago because my Davco wrench was at home. The fuel was right to the top....forgot to mention that in my original post. Anyway, she forgot to put fuel back into the Davco after changing filter...closed the hood. I went out and started it and went in to pay and it wasnt running when I came back out. Took awhile to get it going again

 

Is it possible that the fuel lines are rotting away inside causing the black stuff?
I did have to replace one line about a year ago because it started leaking a bit just before it gets to the tank

 

My shop said they checked the fuel pressure. But i have seen a few air bubble in the Davco before. Not many tho