This pissed me off so much You have to turn off the fan that blows in the center of that room, and the switch for that is in the room with the boss key. If you left it on like me, have fun going all the way back through the level. After you turn it off, drop through the hole in the floor, then use the clawshot to latch onto the metal grate above and lower yourself down into the room to pull the other switch.
