Ok, I am completely stuck!!! After activating the windmill I went and did the 3 bosses behind the statues, but now it seems that I need some extra item to get to new areas. I have 36 cards (filled red gem in all gates I can see) and the girl tells me about cashing them in somehow, but I need to move/destroy/something rocks to go to places. And the village elder just keeps telling me to explore more. Help...?
I can't really help you, other than telling you to revisit areas and look for unopened chests.
At the point you are in the game, there are 37 cards available. I'm surprised you have all the red gems over the gates at the nexus. Have you visited every area? There are only 3 gates you can't access I believe.