Welp, I just got a gamebreaker... the Staff of Nayru, AKA Nayru's Love!
Now, I don't know what the exact requirements are for it, butyou'll at least need the Hammer and the Aurora [Magical] Sword to even get to the room, plus the Lens of Truth to know where to look/what to do. Knowing this game,however, there's probably something more to it.
EDIT: ...Apparently I managed to enter yet another cave from the wrong direction. What I think you're supposed to do is get the third song, play that at a specific dead end in the Past to warp to the "roof" of the Fairy Caves in the Present. The switch that I triggered with the Aurora Sword's sword beam from a distance is supposed to be triggered more manually. Honestly though, I love it when you can solve a puzzle in multiple ways, even if one of the two ways is a bit glitchy.
Either way, that marks three Great Fairies for me. I have Half Magic Cost, Ice Seeds and now the Staff of Nayru. Is that all?
Also, does anyone know how to get to that golden chest just outside Turtle Rock (present)? I seem to remember getting to it somehow, but I forget how >_>
Edited by Neobullseye, 14 August 2014 - 09:04 AM.