heres a mini guide for 2.0.2
The fairy fountain water is directly about the town square fountain in the little cave. (interact with the water itself not the glowing interaction square.)
the topaz is in the temple outside the red boundary. its hidden at the bottom of Temple (basement) by one of the platforms that you need to jump across.
to bone Raegesh you need max strength and then head to the summit of the mountain north of the Haunted woods fast travel point
Vera and the other 2 gems are not in the game yet.