I'm not sure what u're supposed to do with the misc items that are for "extracting essence" such as flowers and stuff like that, does anyone have a better understanding of that system?
Also, need some help understanding what each crystal in the NG+ room does, or atleast a way to keep skills for the new playthro and stuff like that
The flowers for extracting are used in the extract menu when you are trading with Yumir. You can extract most items, even the gacha skills in exchange for essence. You can then use that essence to make direct purchases of skills from Yumir, instead of relying on the gacha for a particular skill that you want. Essence is also needed for crafting and upgrading costumes.
In the recollection room: As for the crystals the pink ones give you options to increase or decrease your lewd stats. The white crystals are shops for skills and items. The Yellow crystal to the left is to increase your exp, the one in the middle gives you more essence to purchase goods, and the right yellow one controls the day night cycle.
As for the NG+ stuff if you are in the room with Yumir with the green and red portals, if you want your skills to carry over it looks like you need to activate the first crystal directly to the left of the green portal or if you look to the right of Yumir it'll be the crystal on the 2nd column, 2nd row from the top.
It looks like those crystals don't actually allow you to keep your skills, instead they seem to raise your proficiency and skill cap.