Narthex/Women’s Restroom:
The only thing you need from that is the manual on knots, so you should be fine.
I don’t think you’re screwed. You are correct about the secondary rooms glitching with the coffee, but I think you just need a fresh perspective on a couple of other things and that will help you get those items you are missing.
Also, when you drop everything, did “Take All” not get them all back? You might want to go back to the Tunnel Entrance/Small Chamber and do that. Or a few other rooms. Maybe you missed or dropped something? (Sidenote: I didn’t even know you could drop Emmett! Any attempt I made to move him got me this response: “It’s not quite so easy to rid oneself of a haunting presence.” )
About the fountain:You said you smashed it, but did you do anything else with it?
Specifically:
[rant]Take a look inside the hole you created. A book you are missing is waiting for you![/rant]
About the Court: You absolutely need to complete this room to get to end game, but the good news is that you probably have all the answers you seek already. You don’t need to replay everything, but you will probably need to read/examine every bit of media you’ve collected. You did pick up all of those random journals, newspaper clippings, recordings, etc., right? I think there were only 2 pieces of info that wasn’t actually listed in something you collected. Specifically:
Uncle Harvawell’s crypt [rant]you’ll learn he’s the Icterine alderman with his weasel familiar[/rant], and listening during the flashback sequence in the cold storage room [rant]would have let you know about Aunt Mavis, the Griveous alder(wo)man and her pet cat, Little Nifty.[/rant]
If you need to know something else more specific, let me know and I can help you out. 
Variegated Court (warning for people who aren’t Dan: These spoil the puzzles real fast! if you don’t feel stuck I don’t recommend them.)
Also, I’m doing these partly from memory, so I don’t guarantee complete accuracy.
Cesious solution can be found in
Milkweed
To find the color (this is redundant, but I’m going to put these in just so you know where the clues are):
read the postcard of Big Ben
To find the familiar:
read the diary of Phyllis Cragne
Familiar is
silverfish
Croceate:
can be found in:
Under the Bridge (the one with the pay phone)
Color/familiar:
read graffiti until you get a phone number. Dial the number (using the coin you found there and stuff). Something dramatic will happen that prompts you to look at the water, which I think you do in the reflection of the payphone. This will reveal the color and give you a glimpse of the familiar.
The first time I did this in this save, the first phone number I got was a red herring. Not sure why. The one you get should be an upside-down cross.
Familiar is:
eel
Icterine:
found in:
Family crypt
color:
I think on the plaque or inscription or something on the coffin?
familiar:
look in the coffin
Familiar is:
weasel
Puce
Solution can be found in:
Padded room
color/familiar:
examine the trophy you got there
familiar is
greyhound
Fulvous can be found in:
Outside the Pub
Color/familiar can be found:
In the newspaper you got from the newspaper machine (“some yellowed newspapers”). (As someone pointed out in the slack, one of the incongruities is that the VC usually seems pretty secret, but here it’s just straight-up in the newspaper.
Familiar is:
Duck
Rufous can be found in:
Meatpacking plant office
Color can be found in:
torn notebook
Familiar can be found in:
the newspaper article you got there, about the dreadful conditions in the plant
Familiar is:
rat
Niveous can be found in:
Locked Office (behind the church, above the basement/tunnel entrance)
Color can be found in:
Journal of Luther Cragne (tiny leather journal you get out of the puzzlebox you find in the locked office
Familiar is a bit tricky (that is, I totally needed someone to explain it to me):
also found in the journal
but not in the text of the journal
examine the journal. Any other part of it you can examine?
Examine the embossed design.
Familiar is:
wolverine
Xanthic can be found in:
Music room
Color can be found in:
Uh, so this one’s super complicated. If you’ve totally finished this, got a message from Francine and everything, and done everything you’ve needed to do in the whole complex including L’Oreille, then you have this. If not, post if you need more hints.
Familiar can be found in:
Again, you have to do lots of stuff to get here…
Have you helped Francine and got a message from her?
Read the police report and keep in mind what she says about her familiar.
The first funeral is the forest you get to if you press all buttons.
The familiar shows up if you visit it after freeing her, I thnk.
Familiar is
peregrine falcon
Also if you’ve got all but one of the pedestals I think you can brute force the other one, since
Francine seems super shitty and I don’t think helping her was a good idea
Griseous can be found in:
Cold storeroom with the peaches and the eyeball
Color and familiar can be found
By reading the message on the wall after finishing the room.
Familiar is:
Cat (or bat, but it’s a cat figurine. At least in my save! Maybe it’s a bat sometimes. Its name is Nifty)
Mazarine can be found in:
Meatpacking plant bathroom (with the horse)
Color and familar can be found in:
Konstatin’s journal
Familiar is:
Firebird
Eburnean can be found in:
Heart of the woods (Jacqueline’s room)
Color can be found in:
The tintype…
…which is in the locket you got.
Familiar can be found in:
Well, it was the thing that grabbed you. Also it’s on the locket, I think. Also it shows up with the color any time you examine yourself in a room where the author didn’t write an “Instead of examining yourself in…” rule.
Familiar is:
Kraken
Fuscous can be found in:
Upstairs hall, north end
Color can be found in:
journal you found in the armoire, or Carolyn’s JogMaster you can get by trying to go northeast when the bricked doorway disappears
familiar can be found in:
either of the same places (I think both will clue you in to both color and familiar
Familiar is
White Antelope
Actually, looking through this thread and seeing all of the questions makes me wonder if someone is already working on a comprehensive guide or walkthrough to Cragne Manor.
I had to make extensive notes and maps when I played through it to finish it. I could clean that up and post it if someone were interested. Is there a desire and place for those kinds of things in this forum? I’m new here so I don’t know how that works.
In case you don’t want that huge spoiler, and following up on ShabyBelle, there’s a total of four Variegated Court puzzles (I think) whose information won’t be found in things you’re carrying around, if you’re carrying everything around.
The solutions can be found in:
Family Crypt, Storeroom, Music Room, Under The Bridge
This would be pretty great! You could make a new thread for it in the “Discussion, HInts, and Reviews” forum here.
That would be awesome. I just finished, & was planning to run through it again to try to get a different outcome from the… spirit-related stuff forced miscarriage. Let me know if you’d like any assistance?
Congrats localmilkhen!
Re: Curiosity Shop; the key thing to do to get the hint turned out to be
to buy something. Duh.
Thank you, dear! And thank you SO MUCH for the help. Now I get to lurk and try to help other people.
I would love that. I’m starting the new thread now and was in the middle of typing up a request for that kind of help. 
As for the spirits, I would be curious to see a different way to resolve that.
For the spirits, check this post.
From a semi-cursory look through the source code, I think there are two endings, and the other one may address the thing you want to address.
If you want to try for another ending without looking at that spoilery post, and want some hints…
It should be available at the end of the sequence.
Is there any way you can get away from the fight?
Any way at all?
“YES! A comprehensive walk-through would be fantabulous! 
”
Done. Are there alternate endings?
[spoiler]I see there’s some choice possible in the Christabell/Carol interaction, but the coffee made it seem like the Observatory outcome was dependent on earlier choices in some way.
I kinda wish the Book of All Days stuff came at the end rather than where it was.[/spoiler]
The only other alternate ending I can think of right now is the horse bathroom.
What needs to be done in the Tunnel Entrance with the hobo by Grueslayer?
I put the candles from the hatch in the sockets and found out the name of the woman in the picture is Cecilia, but now I’m stuck.
Also what can be done in the girl’s bedroom part of the music room puzzle?
If I wait long enough she send me back, but if I return then I find myself in a closet and have one turn to do something before getting killed.
What else around the altar might you be able to interact with?
Try the bricks.
Can’t take them.
You can push them, but that’s not enough.
[spoiler]Is there anything you can use to interact with them more forcefully?[/spoiler
Hit them with the mallet.
Just doing that once does nothing?..
Is there any particular pattern of notes that might be suggested around here?
Anything relevant made up of letters in ABCDEFG?
Solution:
Spell out CEECEE with the notes you play on the bricks.
Something like HIT FIRST BRICK WITH MALLET. HIT THIRD BRICK WITH MALLET. HIT THIRD BRICK WITH MALLET. HIT FIRST BRICK WITH MALLET. HIT THIRD BRICK WITH MALLET. HIT THIRD BRICK WITH MALLET.
One thing is that if you find yourself in a loop of die-UNDO-die, you should use TAKE BACK; this is a situation where you have to UNDO twice to get out of it.
You need an item to solve this puzzle. If you wind up in the closet without it, there’s nothing to be done.
What is she trying to do to fend off the bad stuff?
What does it look like she might need?
Have you found a piece of chalk?
…it’s within the music room puzzle.
Somewhere you might find chalk that’s used to draw on the floor or ground
In the Playground.
Examine every part of the seesaw
If you’re ready to solve the puzzle but don’t know the exact action:
THROW CHALK
Many thanks for that info! Now I need another clue though.
[spoiler]what is the combination for the padlock? AFter listening to the record with the phonograph I thought it might be the number from Peter’s library card, but that didn’t seem to work. The newspaper didn’t give me any help either.
Looking at the drawing of the body that flew in through the window leads me to believe I am to find a second ring to put on Abril’s hand, but where do I find it? The note from the seesaw said something about a circle and mountain climbers.[/spoiler]
Small Chamber:
the first important thing about the newspaper is that it contains lots of articles. Keep reading until you find something that the person who made the hiding place seems to be interested in.
Important general fact about the combination:
It’s four digits.
When you’re able to figure out a date that’s of interest, enter it in M-D-YY format, without leading zeroes.
Music Room (this was something I had to get a spoiler for myself):
The mountain climbers is indeed the critical clue.
Go around everywhere and look for everything that might have to do with mountain climbers.
More general hint about where to look:
It’s in the corridor of the club.
More specific hint:
Check out the band poster.
Just examining the relevant thing will do what you need, but the phrasing of what to examine was a bit tetchy:
You want to examine the logo of the Bread Loaf Mountaineers.
Something like EXAMINE BREAD LOAF should do it.
Thanks for the help! I was able to finish the game!
Is there any use for the old iron key from the science tower or is it just a magnet for lightning?
Old iron key:
The thing that it was found next to will give you a hint as to its use…
The author apparently left a comment in the source code along the lines of “I’m a dick, this doesn’t unlock anything”