Have you found Pit's Arrows? If so, hitting a switch in the glitch area with Pit's Arrows will cure the glitch and put you in a regular version of that area (The Deepest Chasm). In order to get to the Boss Key, you must go north, then east three times from the Deepest Chasm starting screen until you reach the spike room. If you got all three keys from the "glitch" side of the dungeon, then use the extra one on the lock block. Find your way around to that door on the east, fight the Stalfos, then go down and fight a mini-boss. After beating that mini-boss, the way to the Boss Key will be opened.
Make your way to the same area you got Pit's Arrows in the "glitch" version, except go there in the "regular" version. You will fight one last miniboss to get the boss key.
In order to get to the Boss Door, just go through the portal in the first room of the Deepest Chasm. It will take you to a room with a red pipe to the left, and the boss door to the south. Go through the pipe first to give yourself a shortcut to the entrance of the dungeon. Going through the boss door will lead you on a path to the boss.