From the first shrine, go straight until you reach the end and climb the ladder. On the second level, you’ll find another ladder straight ahead, climb to the upper section, cross the wooden bridge and check the right side, you’ll find it behind some sacks.
The second Kodama can be found on a platform below the first dark realm. Ride the elevator first, then about halfway, run towards the dark realm. Go around the wooden planks until you reach the end, you’ll see the Kodama below you.
The third Kodama is on the upper section outside the castle grounds. You’ll need to go pass through one level below the very top area of the prison cells and work your way to the upper section by using the stone platforms.
The fourth Kodama can be found on the watchtower of the gate that leads to the castle. To reach it, you’ll have to work your way through a narrow stone path where you’ll encounter a couple of Dweller yokai and Snowclops. The path is near the second Kodama shrine.
The fifth Kodama can be found at a corner on the east side outside the front entrance of the castle.
For the sixth Kodama, you’ll have to recover the Castle Gate Key first. Once you obtained the key, unlock the east gate and go in the side entrance. Destroy the fourth samurai armor that’s displayed along the corridor.