How are the fuel lines plumbed?
Usually the return line from the rail should return to the surge tank. If this goes straight back to the fuel tank then you may empty the surge tank if your EFI pump is larger capacity than your lift pump.
If the return line is already to the surge tank then my only guess is that the lift pump is not up to the task. Either too small, blocked lines, pickup dodgy/kinked/blocked screen, or maybe that it is sucking air somehow and losing its prime. Funny how it only turns up after half an hour.