If the water pump pulley flange was installed too far onto the shaft, you might be able to pull it out using a small 2 arm gear puller. Put a piece of tape exactly where you want the flange to stop at when you are pulling it. The only other choice is to remove the water pump, and put the pump in a press, supporting just the flange, and pressing it towards the end. Problem is that if you go too far, you will need to disassemble the water pump, and then press it back to where it belongs. I would put a belt onto the pulley before doing anything, and check to see if everything is aligned, and / or how far it is off. If you decide to remove the pump, when you reinstall it, consider using the round spring clamps, instead of the worm gear clamps. The round spring clamp is known as a Corbin clamp, and why I like them, is that they provide constant pressure, and also that they are period correct. Yes, they are a pain to install and remove without the proper tool, so also purchase the proper tool if you don't already own one.