From the Spirit Well, double jump then use Kuro's Feather to glide to the other side. In the Misty Wood, you won't be able to view the map, so I'll just draw some lines instead. With my incredible art skill, you should be able to understand without any problem... :D.

1 - Use Stomp.
2 - Spirit Light Container.
3 - interact with Sein.
4 - Spirit Light Container.

Keep in mind that from here on, the dungeons keep changing when reach a certain area (I'll mark them by uppercase letters).

Before picking up the Keystone, go to #5 first.

5 - Spirit Light Container.
6 - Keystone.
7 - Keystone.
8 - Ability Cell.

Nothing here, keep running toward until a scene is triggered.

Backtrack to #9.

9 - Spirit Light Container.
10 - Spirit Light Container, also a Secret Area #22.
11 - Use Charge Flame to destroy the spirit stone, also a Secret Area #23.
12 - Obtain Climb Skill from Ancestral Tree Tatsu.

From here, you'll have to jump on gloving flowers, but they react to your jump (kinda like on/off mode).

13 - Use Stomp.
14 - Keystone.
15 - Spirit Light Container.
16 - Spirit Light Container, also a Secret Area #24.
17 - Keystone.

Backtrack and follow the path until you reach #18.

18 - Use Light Burst to light the torch.
19 - Spirit Light Container.
20 - It's a hidden tunnel and also a Secret Area #25.
21 - Kill the enemy in the room to open the door.
22 - Open Spirit Gate (requires 4 Keystones).
23 - Pick up Atsu's Torch.

Bring the Atsu's Torch all the way back to the alter.

24 - Restore the light and obtain Gumon Seal.