Alchemy requires you to put in the required mushrooms all at once and then brew it. No need to put them in the exact order.

You use the item that appears in your inventory after brewing a potion to get it's effect.

If you are trying to get True Sight, you eat the mushrooms rather than brew them.

The PC will only attempt the thirsty tree's request if you were caught by a Malice. That quest only becomes relevant once that happens.

That chest is related to the tree that wants a Lilyth mushroom. The Fragile Keys do not work. This is a hint and not the full solution.

Just adding to what VocalRhapsody said in reference to the thirsty tree: Both getting infected with Malice, and triggering thirsty tree's request are linked to the same time of day. More details on that in your journal, but Do Not go infect yourself unless you already have thirsty tree's 'tip'.

Which key did you find? Both are static spawns. One is hidden behind something and the other is within a slime.

The chests location is hinted at in Journal Page 8. It’s location is very memorable at night but you need to dig it up during the day. That chest will then lead to answering all of your other questions. If you haven’t already, make sure to bring a soulfruit to the tree that wants one. You will receive an important recipe for getting that key.

The Manor chest requires the West Wing key to open the door and the East Wing key to open the chest. You have most likely already obtained the item located with that chest and used it for it’s intended purpose. If I recall correctly, it also contained a (Filler) story item.

School Library, Search for the name of the rain dance in their database. Pay close attention to the physical description of 'the maiden'

If you go north and a bit east of the hut, you'll find an orange tree. From the center of that tree, go south, when you hit a red tree, go west. This will take you to the gray scale forest. 

I don't think anyone has spent the time to produce a guide, and Unnie really should be focusing on developing the game itself... 

But if you ask for specific hints, someone can help you with that. (or better yet, join the discord so active players will see your question)