Skip Alcatraz. You'll have better things to do with the time you have. Some suggestions (not totally up to date):
Ride a cable car. Drive & have lunch across the Golden Gate Bridge in Sausalito.
When you go to Monterey, stay in Carmel, maybe at the Highlands Inn or Tickle Pink Inn (I'm not up to date on this, but these are excellent). Drive down on Hwy 1 the whole way.
http://highlandsinn.hyatt.com/property/index.jhtml
http://www.ticklepinkinn.com/
If you have time, you can drive south of Carmel/Monterey to Nepenthe Restaurant. View to die for!
http://www.nepenthebigsur.com/
One good way to enjoy the wine country is on the Wine Train.
http://www.winetrain.com/
I'd say spend a night there. A nifty place to stay is in Calistoga at Indian Springs.
http://www.indianspringscalistoga.com/
Get a couples mudbath at Golden Haven Hot Springs.
http://www.goldenhaven.com/
For dining in the wine country, consider French Laundry Restaurant or Tra Vigne.
In SF, Aqua and Boulevard are very highly regarded.
http://www.aqua-sf.com/aqua/main.htm
http://www.boulevardrestaurant.com/nav/nav.html
Also Postrio, Bix. Great atmosphere at Enrico's, usually live music.
Across the bay, 30 minutes away is Baywolf in Oakland and Chez Panisse in Berkeley is famous.
http://www.baywolf.com/ (tell them I sent you)
http://www.chezpanisse.com/
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