Okay, well I didn't change much, after looking at it more and realizing it's probably more suited for regen capture, which is a slower paced mode, the flow is mainly fine. I did though move one of the ladders to a better spot, remove some boxes in the center, move the statue/pillar thing in the center back a bit for easier access to the canoes in the water, add another plank where one of the oars from the bigger ships meets the deck, so that you don't fall right into the hull, and no-clip the planks on the ground. A bunch of little things but that make a huge difference. Feel free to keep anything or discard it all. Here's the map:
http://www.mediafire.com/download/bu15k7bn55bwh4r/shipwright.ogz