If you're still not getting gas and the pump is working then you may have a clog or crushed fuel line. You may have a blockage at the inlet (sock) in the fuel tank. You may have to disconnect the fuel line and blow it out with compressed air. Make sure the rubber sections are in good shape and not distorted or that the metal lines haven't been crushed or damaged by road debris, rare but possible. Check the line between the pump and carb too. There's not much to the fuel system on an old Mustang so you just have to methodically go through and find what's stopping the fuel flow.
I take it the filter you're mentioning with the "IN" on it is aftermarket as the stock ones screwed into the base of the carb only one way.