I did a similar trip back in 2006, and definitely echo the advice to check out the OBX ferry schedules and try to plan out around it. We had to skip out on Cape Lookout because of the long crossing time between Ocracoke to Cedar Island (we came from the North) and because the ferry only ran every 3 hours. Here is a trip journal that my ex-gf wrote up: http://lighthousefans.com/forums/viewtopic.php?t=605

Good luck and hope you have a great time!