There are two ways to mount an aux tank. In one method, the aux feeds the main tank via gravity (or a separate pump) and the engine fuel pump always pulls fuel from the main tank. This method is often used when the primary fuel pump is mounted in the main tank itself, or if the fuel system uses two pumps (an injector pump at the engine and a lift pump in the tank). If you have a separate engine mounted fuel pump, you can have a Y valve in the main fuel line and pull fuel from either of the main or aux tanks. You may still need a tank mounted pump, though. Some systems may rely on the tank pump to move fuel to the engine, where a separate injector pump handles the rest of the job. You didn't mention the type of vehicle or the brand of aux tank, so we can't guess which system you have.
You appear to have used the Y method and rely on the engine pump to do all the work. It really sucks hard, so you have to have a steady fuel supply to the valve. If you do not, the pump will suck air through even the tiniest pin hole or "wrinkle" under a clamp. You mentioned seeing bubbles when you turn the Y valve, which suggests the valve itself may have an air leak. Can you switch to Aux and then purge the air (disconnect at engine end, perhaps?) and then see if it then continues to run ok?
It appears you ran ok once for 50 miles but the engine pump lost prime after you stopped and was unable to get fuel moving steadily again. Hard to say whether there was no leak initially or you were just lucky enough to have a strong fuel flow and the leak did not matter. After using a few gallons of fuel, there is more air in the tank and the fuel sloshes around more, introducing bubbles.
I'm also a bit concerned about poking the coat hanger up into the aux tank. You probably penetrated a sediment screen in the tank outlet or maybe even a diaphragm if the tank has a pump inside.