Glad you liked Yorna :) You can find the solution for volcano puzzle here. Though I recommend beating it on your own - just use the tablet and follow its instructions to the letter.
No, side quests are still in production. Both alchemist route and factions. Nuns will receive an update and a scene in the next release. I'm also working on fugitives but not sure if I can prepare everything for their own H event.
Yes, I fixed this bug in v0.7. Are you using the public version?