I'd clean the fuel lines, tank and the inlet to the fuel filter to make certain there isn't any obstructions. Bacteria can grow in diesel fuel and create a lot of problems.
When I suspect a fuel issue, I make certain to verify the fuel is clean and there is unrestricted flow from the fuel line. Clean white bucket makes makes it easy to check for fuel contamination.
A very thorough inspection of the fuel lines, including the pickup tube to make certain there are no small cracks.
Report back what you find.
2012 JD855D OPS Black Poly Roof, Deluxe Cargo Box, Front and Rear Protection, Power Lift, Front Hood Rack, Rear Screen (homemade), 800 Watt Inverter, 2500lb Winch installed in cargo bed, Front and Rear LED auxiliary lighting (4" square 27 watt), Front and Rear CV Guards, Koplin Side Mirrors