What I would suggest is that you contact one of the SF Bay kayaking clubs, or go to one of the kayaking rental places (I think there's one in Berkeley marina, and one in Tiburon). Show them a map of the bay and ask them what areas you need to watch out for. They have years of experience on the bay and will be able to point out the more dangerous areas as well as how to read the water conditions.

** tight lines make all my troubles go away **