The other two are the slime and the mimic. There should be slimes dotted throughout the first area, and the mimic is in one of the treasure rooms in the topmost "treasure vault" area of the cavern.
The codex is grayed out because it hasn't been implemented yet, sorry! Same deal with "customized" games, it's a feature I was working on but wasn't able to make available at this time.
Not sure what could be going wrong with the inventory, though. You're accessing the pause menu and tabbing to the character menu, right? When you scroll down to the spell inventory, you can go into it. You can change the second and third spells in the menu, but the first one is your "character" spell-- It's tied to the character you're playing, so it's the only slot that cannot be changed.
Really glad you enjoyed the game though!