The general structure of the levels being intertwined was an idea I had at the beginning and was something I really wanted to push for. My biggest challenge was the first darker level where there was the top / bottom path. I had to make sure that the player couldn't die and go back on the other path and cause issues with the message trigger events.
I agree the hitboxes were harsh in this one. Being new to it all I played with different hitboxes but more often than not it was causing issues with the collision detection of the platform objects for 'containing' the monsters. Defintely an experience thing I want to polish in the future.
Thanks for your input!