I was driving my 1990 ford 150 when I ran out of gas in one tank. I switched tanks and the engine still sputtered. I had to get it towed home. The truck starts but then stalls. I try to press the gas and I feels like I'm forcing in, it backfires and sputters. I replaced the fuel filter and it still does the same thing. I can hear the fuel pum when I turn the engine on. It is fuel injected.
Be sure that both of your fuel pumps are working. You have one in each tank, plus the one on the frame rail by the fuel filter. It sounds to me that you may have trashed your fuel pump in the tank that went empty. The fuel pumps in the tank are cooled by the fuel in the tank & when you run them dry they get hot and short out.