I feel like I've tried everything, but how do you get rid of the mushrooms? It's annoying me that I can't put on clothes.
https://lustdollplus.miraheze.org/wiki/Mushroom_infection
You'll probably need 3 sweet residues to give to Nymosa.
Not really but the quest chain to get her back involves lots of trading items see her and choose the best route for you
https://lustdollplus.miraheze.org/wiki/Finders_keepers
Also, you should get sweet residues from defeating Pitcher plants ( Appear at the inner depth of the forest park) and then collect them with a bottle which the option should appear right after defeating them.
Edit: Apologies for the misinformation I must've forgotten she stays at the temple as I haven't played in a while and just assumed so