It looks like you know what you are doing!
I don't know Yume Nikki, but I like puzzle and exploration for the sake of it, I just think story bits can be a good tool to nudge the player in the right direction.
I've played quite a lot more since then and I am starting to feel I've reach the end of content (some "fillers" items, not a lot puzzle-less pieces nor piece-less puzzles, not much closed door left to open).
You really did a great job weaving the three areas together and it feel rewarding to loop around one and the other to try to bring stuff and states around. There's this feeling of setting up an insane route and trying to unfold it like clock work.
I found a glitch when you use ether next to the red ghost and get possessed, it kept the collisions disabled and removed the ether "leash", with this I found a hidden area I don't think I would ever found.
Clay doll crashed the game because I've just passed through decontamination (-1 index error on hip size).
I am stuck with a purple face huger despite going though all sort of transformation removal. I still not sure if there's layers of transformations that need to be peeled one by one and I'm still not sure what or when some transformations are kept through the day.
I am definitely hitting New game on the next update, try to rework my way there way with my notes.