Northern Coastal & S.F. in 6 days itinerary, input please
 

My DH and I are planning to be in CA from July 4th-10. Here is what we are thinking:
July 4th day of arrival: rent a car and stay at the Cow Hollow, check out GG bridge park and close by areas, watch fireworks, sleep :)
July 5th day - Goals: cross the GG bridge, Muir Woods redwood grove, Point Reyes, Sonoma Wine country
*Where should we spend the night? other things to do?
July 6th-Mendocino-spend the night here
July 7-July 10th~3 days in S.F.~Return rental car
Here are a few places that we would like to check out, not sure in what order...
Fisherman's Wharf
Exploratorium
China Town
Ferry Building
Twin Peaks
any must-sees/dos that we would have time for besides those?

Will someone explain to me the BART and MUNI system? Which one is best for which location? (If it would be easier to be there and experience it that's fine too :)

BART is a train (some above-ground, some subway) system with limited stops in the city, but which goes out to various suburbs in the east bay and south bay areas.

Muni is the bus, streetcar, cable car and trolley system that blankets San Francisco. It does not go outside the city limits, but covers the city extensively. For most purposes, within the city you would use Muni in one form or another.

I have great concerns that you haven't booked rooms for July 5 (have you booked the 6th?)

That is probably THE busiest time of the whole year in scenic parts of CA. I think finding any place that would book for JUST that Friday night would be very difficult. Most places require a two night stay on summer weekends (any weekends) and that is July 4th weekend.

But even if you could find a one-nighter -- I can't imagine a nice place having availability this late.

Another issue - Muir Woods will likely be a ZOO on July 5.

oh boy! I'm glad I checked. I will book those days ASAP. Other than the hotel concern, how does everything else look? should i adjust/add anything?

Where should we stay on the 5th?

Where ever you can find a place. That sounds sarcastic but isn't - really mean it. Any hotel I'd usually recommend is likely full.

I'd start maybe searching Healdsburg. OR - even better, try to stay both nights up at Mendocino.

As I said -- I'd personally avoid Muir Woods that weekend.

good idea. I found 3 vineyards/wineries that i want to stop at, then drive to Mendocino.
Any alternative to Muir Woods along the way? we would really love to see some giant redwood trees

Armstron Redwoods

http://www.parks.ca.gov/?page_id=450

http://www.russianrivertravel.com/parks-armstrong.htm

Point Reyes is a full day(really that isn't enough). I don't think you have enough time to do everything you plan for that day, IMOP.