To begin you must first have, either wrong warped into stone tower temple and then exited and reentered the temple to reset your spawn point, or have used Extended Hookshot to climb stone tower, then used Timestop to cross the gap and enter Stone Tower Temple. There are two ways to accomplish the next part.
For this method a bottled fairy in a REAL bottle is REQUIRED. In the first room on the left after reentering the dungeon, it is possible to use the pushing block to clip Link through the gate that usually opens after pressing down all the switches. To do this you must first push the block until it is one "push" away from the gate(an arduous process). Then lower your health down so that one bomb blast will kill Link. Place a bomb, and right before it explodes, begin to push the block. Link will die and get revived by the fairy, but the block will still be moving without link grabbing it. Quickly get between the block and the gate and hold forward so link walks through the gate. if you do not hold forward, the clip will not work.
The Goron Mask and the Hookshot or Bow are required for this method. Get on the big switch that only the Goron can trigger. Position youself as shown in the video and activate the missile. Press A or the button for the Goron Mask as fast as you can afterwards. (Use Home Buffering for safety) If done correctly you should fall into the next room. Note that if you didn't position yourself correctly you bounce around.
After going down the stairs and into the third room of the dungeon with the 6 armos enemies, it is possible to hit the 2 that are behind the sun block by simply placing bombchus to crawl over the block and and kill them. When you get to the mirror room, punch the first stone in the stack of 3 so it falls to a stack of 2. Next, gainer up to the top of the stack as a zora. Then, do a long jump and grab the sun block on the right side of the room. Transform into a deku and fall, then regrab the left ledge of the sun block so that you are out of bounds. Then simply hookshot the box past the second sunblock in the room and make your way to the door.
By doing Extended Hookshot, you can simply hookshot the crate on the other side of the wall.
If Deku Link has the Deku Sword, it is necessary to perform the updraft room without being a deku scrub since flying as a deku scrub resets Deku Link's B button (if link has obtained deku nuts at any point prior). To get across the first gap, simply roll as a goron and catch the updraft to fly onto the structure straight ahead of you. Then do a long jumpas a zora angled at the structure on the opposite side of the room. Finally, you can either do a long jump as a zora, or roll as a goron to get over the third updraft and enter the room with Garo Master.
By using Extended Hookshot, simply aim at the chest and hookshot it to skip using Deku Mask.
By using Flower Sliding, you can simply clip through the wall and then jump out of the ground to get to the other side.
To do this, you must first traverse to the right side of the first room, and line up with the wall shown in the video. get in the corner by moving left and then rolling until link stops moving. Then do a sidehop, and go into first person mode to easily line up with the wall on Link's left side. Backwalk and quickly pull out a bomb and shield drop it (wait a few frames before dropping it to make sure it drops right in front of Link). Keep backwalking until Link grabs the ledge behind him, then hold L-target and climb back up on the ledge so that Link automatically turns around, the bomb will make Link do a long jump and he will land on the seam of the fence. You then do 4 rolls as regular link; shield drop a bomb; and then do 1 more roll. This will let Link long jump to the switch platform with ease.
To perform this, you must go to the left of the room, backwalk and hang from the ledge of the platform, when climb back on hold L and sidehop right (don't hold right, just tap right to sidehop), then pull out a bomb and when the bomb is above Link's head shield drop it, do a triple slash while still holding L, put on Zora mask and turn left then hold L again. When the explosion boost you off the platform, in midair start holding up and Zora should grab the ledge.
To get the Boss Key Early you must first perform a Ledge Clip at the ledge shown in the video(above the hallway that leads to the boss key). Once you have successfully performed a ledge clip, let go and then QUICKLY hold right and then jumpslash as zora link, if you did this correctly, you'll land on the floor of the room next to the hallway for getting the Boss Key, just simply open the door and go into the hallway.
The second, easier method of reaching the Boss Key early is to first; go through the hallway that has the small key chest switch in it. Kill the hand at the end of the hallway using zora magic and then line up with the rectangular shapes on the wall. Do a vertical slash, and then, in first person mode, line up the center of the screen with the left edge of the rectangular shapes on the wall and then do a sidehop jumpslash. Link will "antigrav" with the ceiling and land on the platform below. From there open the door and enter the hallway that leads to the boss key fight.
Normally Link is required to shine a Sun Block with the mirror shield, or shoot it with a light arrow in order to get the Map in Stone Tower Temple. However this can be overcome by hookshoting up onto the platform which contains a chest, and then doing a properly angled long jump. During the longjump, hold left so that Link is able to grab the sun block and climb over it. After getting the Map from the map chest, backflip onto the open chest, and then do a long jump. In the middle of the long jump perform a Mask Jump to grab the sun block and climb back over.
There is an invisible seam Link can get onto by slashing in a certain angle. After reaching the highest part of the invisible seam, pull out a bomb and well timed drop it and put on the Zora Mask to long jump and grab the platform. Perform another set of long jumps to get around to the center of where the chest is, as Deku Link jump on top of the inverted chest and with caution get near the edge of the chest and turn around. The A button should now say "Open" and link will fall down while opening the chest.
By doing RI under the water to equip the Deku Mask, Link will clip through onto the bridge. From there kill the Eyegore and get the stray fairy.
By doing Extended Hookshot, you can easily hookshot the BK chest and skip fighting Gomess.
You can skip the boss key thanks to the Extended Hookshot. Use the spike bar or bombs to enable FPG. Position yourself behind the Beamos, where the pots are. Aim towards the door, shoot twice then release EHS by releasing L + Hookshot at the same time. Enter the loading zone.