West Coast - Help Me Learn San Francisco Bay...Please...:)

Ok, so in two weeks I'd like to take my first tour of San Francisco Bay and the surrounding areas.
I've been boating for 30 years, I'm extremely cautious (I carry an EPIRB when I go hiking, for goodness sake) and I like to plan ahead while at the same time see new places. I am in Southern California, I know the San Diego Bay and the Long Beach / Newport Beach / Catalina Island areas by heart, but I've never navigated in SF. I grew up there (near Napa) so I know the surrounding land areas very well, but not the water.
I am also aware that SF is no joke. Lots of big ships, shallow areas, narrow channels, currents, lots of things the areas I am in don't have that much of, in comparison.
I have a new 24 foot Yamaha with dual jet drives (handy in shallow water) and would like to maybe launch somehwere near Vallejo, and take a few days (maybe more) touring around. I have an enclosure for my boat, so a guest slip at Pier 39 would be fun, but I'm looking for someone here to tell me where some other neat places would be to overnight or check out. Isn't there an aircraft carrier museum in Alameda you can visit? Maybe a place you can tie up near it? Things like that. This place has all the pros, and I've certainly helped out some newbies headed to my grounds, maybe you can do the same for me...
Thanks,
Gus

Gus,
Welcome aboard. SF is definetely no joke for a small craft. Pay attention to the NOOA site and weather underground marine forecast. FIRST thing to do is get a tide book at any local tackle shop. I take it down and blow it up a little cuz it's so damn small. The tides in SF and Suisun, San Pablo Bay system are wicked at times. Out going tides with a big moon phase can mean 6 knots of rip around the islands and piers, jetty's etc. I was fishing yesterday at the top of high tide going out. Wind was 30 onshore, tide out going meant it was stacking up and snotty.
Small carft advisory's are always likely after 1pm in the entire Bay system due to wind.
With a shallow draft boat you should be okay to snoop around and explore. stay out of the ferry lanes, shipping channel (From the Gate) and away from any oil depo, Treasure Island Coast Guard Station, SF Airport, Center pier of Bay Bridge, working barge cranes and derricks along Bay Bridge, any anchored cargo vessel South of Bay Bridge.....I know I'm forgetting some.
Grab a chart at a local tackle shop and study well. There are numerous places due to 9/11 that are now off limits. The Coasties and US Navy have no sense of humor.
It was a zoo yesterday, Kite Surfers, Sail boats, Ferry's, Tour Boats, Cargo Ships, Coasties, you name it. Be careful, HAVE FUN!

Awesome, thanks!
With some caution, charts and a little planning it sounds like I'll be ok...