I took the 5:45 am ferry when I ran in 2011. The wait didn't bother me too much. I think the ferry was half full at most. Lines stress me out (still had to wait at least 10 minutes for the bus once I got off the ferry.)
One thing that helped me a lot was jogging/running to the start line when my corral was released to head to the start. (I was in corral 3.) This may not apply to you, since you are in corral 1, but you still may need to keep it in mind, otherwise you may be passed by those in the corrals behind you before lining up at the start. From my corral 3 position I crossed the start line 17 seconds after the gun. I had no problem running a good race from there.