Ganon disappears before I get a chance to fight him.

[KiWiSouP]

Link goes into ganons room and holds the triforce up and the room lights up and ganon appears but then he just disappears and the statues keep shooting fire and he dosn't come back. What did I do wrong when setting up the quest?

[Dark Knight]

You did nothing wrong. Ganon is supposed to disapeare, those "statues" shooting at you is in fact ganon moving around the room, just slash in a semi-random fashion and you'll hit him.

[KiWiSouP]

Ah...maybe that's it. There are actually statues in the corners that shoot, but i noticed some of the fire balls weren't coming from the statues so I slashed in that direction and I didn't seem to be hitting anything.

[Dark Knight]

He moves around the entire room, by the time you see the fireball from one area, he's already moved to another. Hence the semi-random slashing, you make hit him in the spot he moved to after he shot the fireball.