1) When you can turn into a dragon. you have to use trial and error to find a place you can morph into your dragon form on the island, but the place I found it to work was in the corridor right before the battle tower entrance. Just go to your throne room, there take the Shrine to the other Shrine on Sentinel island, there's one of those archaeologists there. from there, walk away from the door, go down but when you hit the corridor, don't go further down or you'll get poisoned. Run along the corridor all the way trying to morph into a dragon. Then you can fly around on the island and find the ship in the tree. You can't do this before conquering the battle tower.
5) Before, because you need the Sigil from Deodatus in Aleroth to enter the Hall of echoes. Don't forget to mindread Zandalor!
