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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.

Hi,
before reading, I quote many games moments, which can be felt as spoil for some people (I would).
But there's no hint nor puzzle solution, so read at your own risk.

I really like the game, the style, theme and puzzle design.
So far none of the puzzle felt wrong or bs, when you don't know what to do with something it's because you didn't find the info, if you can't find the info, it's either somewhere or gatekept, if it's gatekept, it's probably for later.
Therefore, what I'm concerned about isn't clues, it's directions.
In point&clicks, you have puzzles that matter now but you don't know it, puzzles that will matter later, and the one puzzle to solve your current bottleneck, you find most puzzle pieces while looking for the one you need right now. When you find it you can unravel / dominos other intermediate puzzles, then choke on a new bottleneck with new zones to explores and still leftover puzzles from previous zones.
The issue here : I don't know what I am looking for. I am seeing probable solutions to problem I don't have.

The diary idea is a good addition but it fell short :
- At some point I had the Kari entry running alone in the lab. I found Kari once, and the entry was removed.
- I had the Yuri entry. Explored the mansion find quite few things (opened the steel door and the paint door). At some point the entry about Yuri disappeared but I don't think I ever found her (maybe it was because I had the school dream with her, which I cannot do again).
- Now my dairy says "..." and I'm blindy reaching around. I'm not hard stuck, just very slowly testing things left and right in the different dreams.
The game is very open and that a great thing. But without direction it's quite frustrating to repeat half of what I did the night before, reach a point I can try something new, wake up or softlocking my night, get by the day, and doing it again.  All without knowing I'm going toward the next thing and not following red herrings or doing things that won't matter before two to three hours later.
Maybe it's just the story implementation lagging behind the puzzles? Did I softlock my save? If it isn't, I am effectively directionless both in the waking world and in dreams. What if my MC is fine with their body and eating titshroom all night ? Did I win the game?
My biggest suggestion would be: keep using the diary to focus the player toward the next big "unlock". Maybe add intermediate entries.

other points:
- I believe at some point the games tell me I can "now hangout with Nanami and Kari", but Nanami says repeatedly that she'll only come up for the coffeeshop. I can't find her anywhere in the afternoon so I guess I misremembered ?
- - At some point Kari must investigate Nanami and find money solution to buy the ... thing for Rin. Did the story lines up for the coffeeshop scene to solve both point or did my game "eat" a scene ? I've worked there a handful of evenings but nothing happened beside stats changes.
- When Rin explain "like in a video game" how the white bar works at night, I can't remember if she explained a way to extend the dream. I ate all my bathroom pills in the waking world trying to figure out what they'll do. I only deducted from Yuri those were in fact sleeping pills. Maybe rename them "Sleeping pills" ?
- The orange "Card lv3" doesn't open the red 3 door. Isn't it just a Card lv2 ?
- There's timing limitations around using the computer, is that really necessary ? Sometime I cannot use the computer before night, but reading the diary and saving are things I would especially do before night.
- Objects descriptions are usually a staple in point&clicks, but so far you've managed without it. For me it's like platformers without "press A to pass through platforms", the bests manage without it and It's kind of a double edge sword anyway. Slow clap.
- I can't process waking world meat or eggs into protein shake, despite it not having to be complex and now I'm scared they'll mince me instead ;)
- (though "mince you instead" would reference their cold colleague's hand, but you cannot "shake" that hand either)

- Loved the Doom movie reference :D

Really nice work!
There's one detail that hinder the experience: buttons don't extend to the frame there in and only the text is clickable. They are kinda small already but they are even smaller than they look.
I'm not proficient in python/renpy, therefore I don't know what you're working with, I tried doing something like and seems to fix the issue for the sell all button of the cargo:

Nothing that can't be fix with a big find & replace

Good luck and Happy holidays!