I've been taking a look for hours trying to figure this one out, it was really tricky. Sometimes if you bought stone before you need it a quest wont trigger correctly, it's very silly. I'm really really sorry about this, I'm trying to test and prevent issues very often but there will always be something getting through. It's my fault.
I have made this fix for you which should hopefully make the quest activate properly. You can just rewrite the file in your "games" folder. THEN - you need to go talk to the Keeper in his mansion again and ask "So what are those beacons you mentioned, can they be crafted somehow?". Then the new quest should be active and you can finish all the Emily/Witch trials which after you finish them all will result in Amelia giving you a compass when you return home.
Sorry again for the inconvenience, I would be really sad if you don't experience the rest of the game since it only gets better from there. If you encounter any other issues I'll try to help, and if this fix doesn't help you I will just edit your save file so no worries.
