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To review - - the fuel pump in the tank pumps fuel to the injectors. There is a fuel shut-off which works in a wreck to prevent a fire. If the plunger is down, the switch is on. Normal.
It is possible the fuel lines are full of air which would take a long time to purge by cranking the engine. Sometimes you have to use starting fluid or other means to "run" the engine long enough to get gas back into the injectors. As long as the engine cranks, the battery is fine. It is also possible the pump was damaged when the tank was run empty. The pump uses liquid fuel to cool and lubricate the electric pump. It can overheat when running the tank below 1/4 full. It is also possible the fuel filter was clogged with junk from the bottom of the tank. I would get someone to check for fuel pressure at the injectors and try some carb cleaner or starting fluid in the intake hose next.
Turn the key to the ON position without starting the engine. You should hear the fuel pump running for 5 seconds if working. This primes the gas to the injectors when doing this. If not heard running check the oil pressure switch for the 12 volts needed to run the fuel pump starts there on that harness. When the engine starts and the oil pressure reaches the normal pressure the computer shuts off that circuit and turns on the fuel pump relay to run the pump. The relay stays on till you shut the engine off
This is usually caused by the temperature difference between the Gasoline in the fuel station ground tank, and that of your fuel tank. Without spending money to improve on your fuel tank venting system,,the only thing i can suggest is to pump the fuel in more slowly.
The fuel pump reset button is the only thing I can think of to try when your problem occurs. As for your mechanic, believe it or not, might not tell you everything he knows until you guarantee him the work or his equipment isn't able to get the codes that a dealers can. If you have any warranty at all I would make sure that if you have anymore problems to take it to the dealerr and let them do their job. And another thing that might not be related, but is very important on Ford vehicles is that you secure the gas cap completely or it will set a code for that alone! Ford suggests in their manual 3/4 turn or better after the clicks, but it's best to do it until you can't stand it anymore.