Air leaks can cause rough idle, shutdowns on deceleration, and no-starts. The time required for air intrusion to make itself known depends upon the proximity of the leak to the transfer pump. For example, the engine might start and run several minutes before air entering from a fuel tank connection reaches the pump. Air entry closer to the pump has more immediate effects.
Multiple leak points—Schrader valves, bleed screws, fuel-line connections—make the filter/water separator a prime suspect. Use OEM clamps on hose connections, new seals, and dope screw threads with sealant. Surplus fuel from the injectors recycles back to the filter. The connection at the filter incorporates a check valve that closes when the engine stops. Should the check valve leak, air from the return line will be drawn into the filter as fuel in the canister cools and shrinks.