Crimsonphoenix

I've tried going back to the boat to repair it but it won't let me repair, the message says "You don't need to mess about with broken ships now that you've found the secret passage from Karamja", but when I went to Karamja and found the door it won't let me go through it.

I was killed by Elvarg during the quest, Ned won't sail me back to Crandor, but when I went to the Karamaja dungeon the door won't open. How can I get back to Crandor?