You need to get the battle tower first, so you can fly to the ship in the tree. BTW, you may want to read the book yourself, rather than complete the quest (can not do both).
The mine tower in Broken Valley can also wait until after you have the battle tower. Everything else in Broken Valley and Sentinel Island should be completed before you finish off the tower (there is a warning), since many places and NPCs in those areas will become unavailable.
