On my E39 I had issue 3 too. My 530d had 3 fuel pumps;

- A pressure pump located at the bottom of the car near the driver seat
- A feed pump in the right half of the tank
- A leveling pump in the left half of the tank

In my case the leveling pump died. The remaining fuel in the left half of the tank was "seen" by the gauge but inaccessible due to the defective fuelpump.