With the help of Great Bay Early it is possible to obtain the hookshot before entering Woodfall Temple. In the second room of the dungeon, simply hookshot the torch on the pillar near the switch that spawns the ladders. Then jump up to the higher platform. This skips everything in the dungeon between the second room and obtaining the Bow. It is also possible to use the hookshot in other places such as the beginning of the dungeon and the room before the boss fight to skip flying around as a deku scrub.
Using Hookshot Clipping it is possible to clip into the wall separating the fight portion of the room and the portion with the Boss Key chest. After knocking the Toad off the Turtle, push him as far into the wall as possible and then target the wall and sidehop into a hookshot clip. After you clip, you'll need to jumpslash to get back up to the floor on the other side.
Thanks to EHS, you can get past the door that leads to the boss. To perform the boss key skip, you want to stand on a specific platform, enable FPG then shoot your hookshot until the chain goes through the torch and it hits the door. From here, release EHS by holding L + Hookshot and releasing them at the same time.