The symptoms you describe imply a fuel restriction. These can be caused by debris in the fuel tank, condensed water freezing in cold ambient temperatures, use of summer blended fuel in cold ambient temperatures (waxes precipitating out of fuel), bacterial sludge in the tank blocking the outlet strainer or various downstream components, non-functioning left pump (if installed) etc
Start at the fuel inlet line to the injection pump and using a container to catch the fuel, open the tank valve. Do you have a gush of fuel or is the flow intermittent or just dribbling? If it is not a gush, then work your way back to the tank outlet until you get full fuel flow and then you have found where the blockage is. If you have a lift pump, make sure it is working to supply fuel. Some have a screen in them that can clog, or they can fail.
Water in the fuel occurs from condensation (assuming you don't leave the fuel cap off) and is the start of bacterial sludge as the microbes live in the fuel/water interface. No Water, n bacterial sludge. You can't eliminate condensation but you can minimize it by keeping the fuel tank full of fuel between uses. Drain your fuel filter regularly and look for water in the drainage. If you have a water separator, drain that also. Treat you fuel as it helps the water accrete on the filter and then slide down toward the bottom to be drained.
If you have a solenoid on the injection pump (IP), Make sure it is functioning properly. There are usually two solenoids; an opening solenoid and a holding solenoid. They are both on when starting and the opening solenoid shuts off in the key switch run position.
Systematically go through the fuel delivery system and you'll find the problem.
Hope this helps.