I love Sheikah threads so much!
Some more theories on the shadow temple.
The Shadow temple, Bottom of well, royal graveyard, and race for hookshot area are all (IMO) Connected. Not litterally but they're sheikah tunnel systems. The man who lived at the well is definatly sheikah. Weather he's good or not, I can't tell. But Many believe the sheikah were the interlopers so we can't look at them as these perfectly good people.
The sheikah and the fourth god...
The "TetraForce" Theory
Focuss on my posts since some think the fourth god would represent the gerudo
In the royal graveyard you learn the sun's song. The sheikah dug the grave and they probably wrote the song. Back to the whole goddess of time thing. The door of time and the blocks have a shining sun on them, sun's song relation? A Time block blocks the exit to the place you get the hookshot. Does the song of time relate to the sheikah? You get the hookshot from Dampe but his journal suggests he found it. He digs graves in the sheikah graveyard so he probably found it with a sheikah body. More evidence of the hookshot being a sheikah item is that it's needed to get throught the first part of the shadow temple. Anyone have any idea on the hover boots/