Running a fuel pump dry makes it lose its prime, also may damage the pump internally. This is common for a fuel pump with some miles on it and running out of fuel. More than likely you might need to replace the fuel pump.

As far as sucking up "gunk", that is also possible. When I did mine there seemed to be a lot of mud like substance in the tank and fuel pump. There are 2 strainers in the fuel pump assembly itself and that is most likely where the blockage would be if there is any.

Good luck!!