Hi,
Not sure if I can answer any of your questions, but I live out here so I am going to try to send you in the right direction.
I think you will need to rent a car to do all the things you want, try to get a good deal with a rental at SFO. Sonoma county generally will be cheaper than Napa county, but with a car it is all doable.
Do you belong to any hotel chain programs? If so, you can use points to get a cheap hotel, especially if you stay just off of 101, which is convenient, but not always scenic.
Here are some local maps/site ect for you to look up. (all for Sonoma county)
www.sonomavalley.com
www.wineroad.com
www.sonomacounty.com
Hope that is some help, fall is a great time to come out to wine country.