Yep, Vagullion is infamous, and the bane of many players existence. Its probably the longest boss fight in the game based on how its attack pattern works. May I ask what difficulty you are playing?
I think the only other boss that poses a serious challenge is the last boss.
The strategy for Vagullion is pretty simple, but regardless, the fight takes a while. When the fight stars, move closer towards the boss and when he transforms into the smaller bats, follow along the edges of the room in a clockwise or counterclockwise rotation. When the swarm starts spread out, The goal is to keep as close to the swarm of bats as possible as the boss will pull them closer into a group to chase you that will be easier to avoid then the spread out bats. The problem areas will be the corners when the tiny bats are spread out. Make sure not to stay to too far ahead as periodically the boss will pull the bats in and form his true form. Thats when you have a very short window to hit him. When he turns into bats again, try to get close to the walls and continue the clockwise or counterclockwise rotation. Keep up the pace and you will eventually wear him down with minimal damage.