Well I found another stone on some fire golem thing. Just about finished with the first map. Mainly just the temple left.
But I did go back to the Black Cove and checked the chest in the boat near the pirate boss battle and nothing is there. I would have sworn there was a stone in Black Cove. Would love to know where it is. I reunited the headless ghost with his head and the woman ghost with her husband in the lighthouse. I just can't think of anyplace else to look in the Cove.
So right now I have two pyramids and three inert stones. The stones I got from the clinic, the murder room and that fire golem.