The Santa Cruz/Monterey area can be fun in October. You note Carmel, but as mentioned could be extremely expensive. The Monterey Bay Aquarium would be worth a visit,
http://www.mbayaq.org/ The Santa Cruz Boardwalk is worth a visit coming from Kansas.
You are talking a pretty big distance from Napa to Carmel though. To cover all the area you note you will need a week.
I second the ferry comments. If you are staying in San Fran, take the ferry across to Tiburon and drink/eat at Guaymus.
www.guaymasrestaurant.com More if I think of anything.
No idea on the staying part of the question.