The Shrine is accessible from Great Plateau Foothill Cave beneath the Great Plateau surface. Entrance of the cave is towards the North of Great Plateau at -0832 -1488 0027. Once inside the cave there is a large number of crushable stone walls to go through to reach the shrine, bring lots of weapons or Bomb Flower.
Alignment of the Circles
To complete the Shrine simply place the orbs in the receptacle below each green circle on the ceiling.
Video Walkthrough of Kyokugon Shrine
Place the orb in the hole to reach the chest that contains a Hearty Elixir