Fuel tank, lines question

My Cj5 (built 10/66 with V6) came with a fuel supply line (bottom) and a return (top). After a restore when I hooked the supply line to the fitting on the tank bottom and the return to the top fitting, it would not run. I looked inside the tank and the supply tube was bent over, flattened, and brazed or soldered to the inside of the tank. No fuel could get out or in. I swapped lines and pulled fuel from the top fitting and essentially dead-headed the return line. It has been running fine this way for a year. However, I have noticed that the fuel pump is pretty noisy. Am I harming anything running like this? Has anyone else seen a tank done this way? I know the original owner and am pretty sure no one has ever had that tank out before me. Thanks!