Sometimes when you run them dry you suck up all the gunk at the bottom of the tank, and plug up the filter. Start at the tank outlet and make sure fuel is flowing. Then follow the lines from there all the way to the injectors and check fuel flow at each possible problem area. I'm not sure how that engine is set up, but generally speaking, check fuel flowing out of the tank, then out of the lift pump, then out of the fuel filter, then out of the injector pump (or just at the injectors.
Regardless, I'd put a new filter in it because there's no way of knowing what came out of the bottom of the tank.