By using a well positioned bombchu, it is possible to activate the crystal switch at the top that activates the shortcut to the top of the room. This was fixed in the 3ds version of the game by changing the switch to a press switch.
In the block room, it is possible to hookshot the target and get pulled past the glass wall, allowing early access to west courtyard and the crystal switch that controls the twisted hallway.
It is possible to climb up through the web in west courtyard to gain early access to east courtyard without having the bow, allowing earlier access to small keys.