From the main entrance into the trial room, use the deku leaf to glide from one pillar to the next, and make your way over to the Forbidden Woods trial door. From the last pillar glide and land on top of the trial door. Walk towards either edge of the door frame until Link grabs it and pull yourself up. Now pull out a bomb and use it to ledge clip out of bounds. Be careful to quickly move away from the bomb before it explodes and hits you and glide to the loading zone.
In the main room at the beginning of the Phantom Ganon battle, preform storage. Attempt to open the door on the left of the central door that leads to the grand staircase. The door will not open and you will have stored it. Head to the opposite side of the room and open the door. Now return to the previous room. You will notice that the door the you tried to open with storage activated is now open. Jump through it and glide to the loading zone.
Head over to the room on the right that leads to the Phantom Ganon battle and wait for the cutscene to finish. Head over to the left near the drop off by by the stone. There is a little indentation which when you run towards will allow you to jump without falling into the Phantom Ganon battle. Once you have found this spot, run off it and use the deku leaf to get on top of the stone.
Set a bomb down and then pull out the wind waker and cancel it so that it is still in your hand. Now here comes the tricky part, getting a wind waker dive off of the bomb followed by dry storage. Sometimes you can simply flick the control stick towards the bomb at an angle and mash the button your wind waker is on to get the dive. Once you have gotten it, cancel the wind waker just in time to get dry storage (pause buffering may help with this).
Store the text from the stone and run back over to the door. As you press A to open the door, the text from the stone will pop back up. Quickly mash through the text box to keep the door from closing. Now run over to the door on the opposite side of the room, watch the cutscene, and return to the preceding room. Run through the open doorway and leaf pump to the loading zone.
Note: Because of the difficulty of Puppet Ganon Skip, this is most likely TAS only, or for use in a segmented run.
At the very top of the grand staircase, align with the pillar on the left as shown. Backflip and pull out the deku leaf. Just as you are about to hit the ledge, put the deku leaf away to grab it, and shuffle your way as far to the right as you can go. Now climb up the ledge and immediately jump towards the wall to clip through it. If you wait to long Link will simply fall off the ledge and you will have to start over. From here, make your way to the loading zone, being careful not to fall.
In Puppet Ganon's chamber, angle yourself towards the path that leads to Ganondorf. Deminish you health to 1/4 heart and zombie hover. This is a mostly luck based hover, as the conditions have to be perfect in order to prevent from getting knocked down by the Keese. Once you are above the red wooden entrance to the Ganondorf battle, wait for a few Keese to come and attack you. Equip the deku leaf and bombs. Quickly press the button the bombs are on, followed by the deku leaf, then B. If done correctly, you will drop a bomb and get a heart drop from the Keese.