Are you sure you are testing voltage right, good connection and good ground?
I would think you should have 12V to the pump, but just running out of gas should have no effect on voltage! If it ran fine before running out of gas then it should run now.
Are you testing with pump un-hooked, or trying to run the pump while testing for volts? Another thing is if there is a load on a line, like pump trying to run, sometimes you will see lower volts on that line due to the load.
Since I can't see what your actually doing just guessing in the dark here.
Since you say it worked after connecting pump direct to battery this is odd. Now that you have it running have you tried connecting the pump back normal and see if it still runs? Could be you just had lots of air in there and took long time to fill the float bowls?
Or since you said you saw little gas, maybe you never really were out of gas and something else messed up like low volts to pump, maybe a bad wire/connection somewhere.
Not sure about the 1200, but the 1500 you can't really see the bottom of the tank anyway the way it is made, and sometimes people think they see bottom of the tank and empty when in fact they do still have near half a tank left.