Start by changing your fuel filters. If that doesn't fix the problem then I'd say it is air in the fuel
engines, 90% of problems such as this is the result of air being sucked into fuel lines or the fuel filters. Check all fuel lines & clamps; check your water
separator fuel filters, especially the o-rings in the top & bottom. Sometimes the old o-ring is not removed when changing filters and adding a second one allows air to be drawn in.
One way of tracking down the source of air is to temporarily install a section of clear hose and check for small air bubbles. The leak is somewhere upstream of wherever you see the air. Work your way through the system methodically and you will find the source of air intrusion.