When the fight begins, roll up the ramps, staying close to the edge to keep from getting slowed down by the walls. If you roll quickly, you will easily out run Helmaroc King. Once you get to the top, select one of the following strategies according to the conditions of your run.
Note: It is also possible to preform a storage-less superswim in the water at the beginning of the room and to build up enough speed and momentum to carry you all the way up the ramps and behind Helmaroc before he has time to land. This is, however, only really viable in a TAS.
After you have pounded Helmaroc King with the Skull Hammer and he has fallen, pull out the wind waker and get dry storage off of the ledge in front of you. Now climb up to the top and trigger the cutscene. Due to the fact the you preformed storage, you will be able to walk around during the cutscene. Now jump back down to the bottom where the battle began before the top of the tower closes (which still costs a 1/4 heart).
Once the cutscene has finished, pull out the wind waker and then press the button it is on again to fix the camera. Roll up the stairs and get on top of the first wooden cell by the stairs while waiting for Helmaroc.
Note: This is the risky part of this strategy — there is a high risk that after the cutscene of the roof closing ends, Helmaroc often gets stuck in the sides of the tower while trying to get to you. Due to this, this strategy is probably best utilized in a segmented 100% run.
When Helmaroc lands and comes over to peck you, due to the fact the you are on top of the cell and he cannot reach you he will continue walking forward infinitely. This means that you can even pound his head with the Skull Hammer until his mask falls off and he will continue to walk forward. Be careful after his mask falls off, as the properties of the cutscene will clip you into the wall. From here you can simply use quickspins to finish him off.
After the cutscene of Helmaroc's death is over, you will automatically be warped on top of the tower — free to grab the heart container and proceed.
After the third time you have hit Helmaroc King with the Skull Hammer, lure him into the corner near the spikes. After he pecks at you, and gets his beak stuck in the ground, hit him once more with the skull hammer. This will trigger his 'unmasking' cutscene, which automatically warps you to his head. This clips you past the spikes allowing you to skip his second phase.
Once at the top of the spiraling walkway, sidehop and use the deku leaf to grab the platform behind the Helmaroc King. Align yourself properly, and zombie hover towards Ganondorf's look-out. Hover to the loading zone behind the door and proceed.
Skip the first hit in the same way as told for the long hover, by leaf to the ledge behind Helmaroc. After this, take up the rock nearest the spikes on the right side, since this one contains hearts. Make sure you only have one quarter of a heart left. Line up to the spikes and place the rock behind you. Take out a bomb and place it in front of Link, between him and the spikes. Turn around quickly, take up the rock, face the spikes and throw it. If lucky, one or more of the hearts will get on top of the spikes. If so, let the bomb kill you and zombie hover towards it. If you get it, you can jump of the spikes and run up to Ganons door.
Note: The hearts in this trick is totally luck based and might not land on top of the spikes 100% consistent. But, this is the fastest way of skipping the fight by console.
Because of the timing necessary to preform this trick, it is considered TAS-Only. More info to come.