I don't think that's normal, haven't ever had to enlarge a pulley hole to fit. Yes you need to fix that pulley alignment with that much misalignment the pulley wobble will knock out the water pumps front bearing quickly. Did you make the center hole big enough so that it will side onto the pumps shaft easily? Does the water pumps front flange look like its pressed on straight? i.e. 90 degrees to front of engine. If pumps flange is straight then it looks like it wasn't pressed on far enough so that pulleys will line up correctly compare its height to your old water pump, then maybe you should have them get you another pump that correctly built. Good luck