When you run out it takes some time for the air to bleed out. Don't forget the gas intake is in the bottom of your tank, and rust and water sinks in gas so if it was in your tank when you were empty it was in your tank when it was full, and it would already be in your fuel filter. If you let it sit for a while empty then you can get extra condensation, but running it empty then filling it shouldn't have a huge effect on condensation. I wouldn't go crazy and tear things apart. Just drive it for a tank or two and put some water displacement fluid or gasline antifreeze in it and see how it goes. When you run out of gas you run out, and it won't start right away. It doesn't sound like you ran out, but it possible you could have sloshed aroung whil almost empty and sucked in some air.