Cm2250 Won't prime/no fuel in water separator

[HamblinTrucking]

Ok, I've searched high and low and I can't find anyone who has posted about my exact issue.
First,
2012 Cm2250
Freightliner Cascadia
Davco 382 water separator
New check valve in separator
New cap and seals separator
New primer/lift pump
New filters twice

My truck will not draw fuel into the water/separator. It occasionally will and did with the new water separator filter today. If I fill the bowl and run the truck, I can feel when It gets back down to the edge of the housing. It draws just enough fuel to pull but not great. Boost drops under load from 35 to 30 then after a while will go from 30-25.

The check valve had some trash in it and I changed it. I also replaced the fuel primer pump. I have checked fuel pressure with the primer pump and it's around 30psi. I let the pump run and pushed in the compucheck fitting and a ton of air came out of the high pressure filter. When I let the primer pump run and then shut off, I can hear air ( possible being drawn in) around the high pressure filter-ish area. There are no leaks under pressure though.

The truck has always had a weird howl noise on the driver side and the best I can figure is, it's something to do with the fuel filter. It only does warm and from 1400 rpm and up. I also have been fighting filters getting black in 5k miles or so. I've been using fppf killem and not really any results. I would imagine the fuel is just getting really hot.

Now, what I have done is verify that the lines to and from the tank are clear. They flow just fine. I have not checked the check valve In the intake side of the primer pump, nor the screen on the gear pump.

I don't have any codes. The truck just runs a little weak. It has a newer gear pump and injection pump. It also has that locomotive sound like one cylinder is either hitting harder or weaker. It's uncomfortable to me and I know it needs fixed. Please help!