Sail to the left side of the entrance to Forsaken Fortress. Climb up onto the rocks and walk over towards the blocked entrance where the rocks dip down. Now walk towards the edge and pull out the Wind Waker to Wind Waker Dive. Wait about until the first count on the Wind Waker's scale and swim over behind the large wooden door. This not only skips first obtaining the Skull Kammer and battling Phantom Ganon, but also skips the intro cutscene into FF2 as well.
After getting to the pictured searchlight, call Tingle and make sure that the wind is blowing southeast. Align yourself with the appropriate angle and zombie hover. After starting the hover equip a red ting to B on the Tingle Tuner. Once you have passed through the wall above the door to the Helmaroc King battle, press B on the Tingle Tuner. Right before Link is given the ting, tap the Deku Leaf button and leaf into the loading zone.
Once at the top of the spiraling walkway, jump and use the Deku Leaf to grab the platform behind the Helmaroc King. Now perform one of the various Helmaroc King skips and complete FF2.
When sailing towards Forsaken Fortress, stop at Child Isle and perform Dry Storage. Sail northeast of Forsaken Fortress until you see an outpost. Get Chest Storage on that outpost and sail to Forsaken Fortress. Walk up the walls and you will walk through them and fall into the water, similar to the above method. Get back on ground and walk past the Phantom Ganon cutscene trigger. Now simply walk up the walls as shown in the video below and enter the loading zone. Skip the Helmaroc fight as detailed above.
Part 1 - Make sure that the tingle tuner is activated, with a red ting on B. Lower your health to 1/4 heart and position yourself towards the ledge on the right on the large central statue. Zombie hover to the ledge and heal yourself using the ting once you're above it. Call Medli with the Command Melody and use her to ledge clip through the wall. Get back up while OoB, pick up Medli, and jump behind the statue. From here, proceed to the room with many floor masters and get the small key. Now, let the floor masters take you and Medli back to the main room. Call her with the command melody and use the key to unlock the door. This skips having to hit the peg with the skull hammer in order to obtain the intended key.
Part 2 - After getting the Mirror Shield, go to the third room in the dungeon, and reveal the treasure chest. Preform storage and open the chest. Now return to the statue room and call Medli. Navigate your way to the fog room that contains the peg that you would normally hit to activate the light ray. Navigate to where the peg is and place Medli near the wall and use her to ledge clip OoB. Glide over below the floor of the next room and use a tingle bomb to boost yourself up onto it. Now use the command melody to move Medli as close to the grate as possible. Because chest storage allows you to clip part way into walls, you can pick her up through the grate. This allows to bypass the locked door whose key you used to get to the Mirror Shield. Now carry her over to the statue blocking the door and use the same aspect to place her inside the statue. Jump and glide onto the pillar that is to the left of the statue. Backwalk into the wall and grab the ledge to ledge clip OoB. Glide over into the doorway and call Medli with the command melody. Pick her up and open the door to proceed.
Make sure the wind is blowing north, call Tingle and zombie hover above Gale Island. Mid-hover, equip a Red Ting to B on the Tingle Tuner. Alternatively, you can hover to the hearts on the island to the side of Gale Island. Once you are above where the wind is blowing from, use the ting to heal yourself. Walk over to the ledge on the right and backwalk until Link grabs the ledge and clips into the rock face. From here drop down and immediately use the Deku Leaf to glide over the loading zone.
Note: There is also a peg that you would normally need the skull hammer to activate in order to unbar the door in the Mini Boss room so that you can exit. However this requirement is easily overcome by save warping back to the first room of the dungeon.
This is one of the simpler times in skipping the Skull Hammer requirements. Sidle part-way into the gates and roll the rest of the way through. This is the only place in the sewers where the skull hammer is normally a requirement, as well as the only time when skull hammer requirements are impeding skipping it in the Triforce-collecting sequence.