Of all the items in The Wind Waker, one of the most useful is bombs. Bombs can be obtained in any pirate ship as long as you triggered the gossip stone text in Forsaken Fortress 1, because that text is the trigger for the pirate ship to have rope game 2 instead of rope game 1.
If you have the grappling hook when going through Forsaken Fortress, you can Item Slide to the pirate ship behind the outer rock after obtaining the gossip stone. The gossip stone is the trigger which sets the pirate ship to be in its next state when it has the bomb chest and rope game 2.
After you obtain the grapple hook, you can Item Slide and superswim to Greatfish Isle with relative ease. If you have completed Dragon Roost Cavern and have the Wind's Requiem, you can set the wind to south after the Greatfish cutscene to trigger being able to enter the King of Red Lions. When you enter the King of Red Lions he will autosail you to Windfall since you haven't completed Forbidden Woods yet as completing Forbidden Woods is the trigger for being able to sail anywhere on the great sea. After watching the Greatfish cutscene, the pirate ship will spawn on Windfall.
Note: In a TAS, it is possible to perform a superswim without item sliding. Because of this, you can get the bombs directly after completing the first visit to Forsaken Fortress.
After you obtain the grapple hook, you can Item Slide and superswim to the Flight Control Platform. While playing the minigame, it is possible to angle up and Island Hop out of the quadrant to dragon roost island and perform an Item Slide Superswim to Outset where the pirate ship will now be. The reason for this is because the Flight Control Platform minigame takes place on an overworld layer (state) which also happens to spawn the pirate ship at both Outset and Windfall. Once on Outset, you can simply item slide to get on the pirate ship and enter it. If you decide to go to Windfall, you will have to perform Password Skip to get inside, since this pirate ship is password-protected. Because the layer resets when Link savewarps or drowns, you must reattempt the island hop if you fail it.
A TAS would be able to island hop directly from the Flight Control Platform to the loading zone of the pirate ship before the collision has even time to load.