I'm wondering if the witch is buggy... I'm having a lot of trouble getting a raptor for her (in the lake... the scene mentions the raptors being easier to capture, but there's no option to take it), and I have a similar amount of trouble finding the alpha werewolf (during the day, in the forest).
I also do have the prisons all built, and I've gone pretty far in my quests. I tried taking the raptor quest maybe a little earlier than usual, maybe, but I ran into the same bug as mentioned earlier, and had to abort it to move on.
Also, one tip for those who have trouble finding glowshrooms; if you want, you could just grow more. If you grow a garden, you can get 10 more in a single day just by planting the one you find in the cave.
This game is really great so far. The writing is pretty damn good, and it feels very polished and full-featured compared to other RenPy VNs. The gameplay is engaging and varied, and I've spent... Probably 20+ hours playing it so far, and there's still stuff I haven't explored yet. Probably got another 5-10 hours of gameplay that's currently finished for me to explore soon, and I look forward to seeing your updates!