The flying minigame rewards you with a heart piece, and so is required for 100% speedruns. First, make sure to have the wind set to North-West. Start the minigame. Pull out a bomb as soon as possible. Jump as soon as the bomb explode (or a little bit before then). Hold up on the control stick and that's it. You will catch one tornado, and that's enough to make it to the finish line.
This strat is comparable timewise with the strat above if the North-West wind direction works for you. You can escape the minigame once it has started using a bomb boost. Once back to the entrance, enter KoRL while making sure to NOT touch the water. Then sail over to the finish line. Once past it, play the Song of Passing in order to reload the area and jump into the water. This will count as a win.
After playing the minigame (winning or losing doesn't matter), the overworld is put on layer 1 on the japanese version and ONLY the japanese version (this was patched on NTSC and PAL). On layer 1, FF is automatically FF2. This is useful in order to obtain the Skull Hammer after Hyrule 2. By playing the Song of Passing on layer 1, you can access layer 0. On layer 0, the pirate ship is there on Outset (it might not be textured though), and FF is in a broken state where the door leading to Helmaroc isn't there. See the Layer Manipulation EMS method.
By performing the Flight Control Platform Escape trick used for the cheese strat, you can get into KoRL while the minigame is happening. The minigame takes place on layer 2. On layer 2, FF is automatically FF3 (which is useful since the Dark Portal linking FF and Ganon's Tower only appears in FF3), and the Pirate Ship will be on both Outset and Windfall.
Playing the Song of Passing while on layer 2 puts the game into layer 3. Layer 3 doesn't have anything notable that the other layer manipulations cannot already do.