Dude, you're going about this in 100% the wrong way, lololol. Can't believe you even got your way to work.
Hint: It's atrial.magnesis
lol, i know it wasn't the correct way to do it at the time i was doing it, but i thought it was pretty fun throwing bombs in the water to launch the balls
edit: so after receiving all of the runes in the beginning of the game should set me up for every other shrine in the game?