Hi
I was hoping that someone else would answer to your question because i did not understand everything !

Did you cured Elder Anlokam ?
Did you find the crystal fragment and solved the necromancer's last task ?

If yes you have the whole crystal and Elder Anlokam will teleport you to the Raanaar Academy.
You don't have to use the stairs to go out or to use the pyramid to finish the act 3.

Barta