B.M.
What a great trip. We did this last year. I of course was pregnant and couldn't enjoy Napa like I wanted to! Napa is actually something that probably takes more than 1 day, but definitely go to Domaine Chandon and take the tour while you are there. I am sure there are a TON of wineries that are great, but I really enjoyed this one.
When in San Fran . . .Scoma's on Fisherman's Wharf (pier 47) is excellent if you want great seafood. As for the alcatraz tour . . .I have heard great things about the night tour. We couldn't get in, but we did hear that you can order your tickets online before you go if you know what night you want. I would actually suggest that. If you do a google search for "alcatraz night tour" there are several sights that offer them. Not sure which ones are the best though. We did get into the day tour and that was great, so if you can't get into the night tour, the day one is good too.
We did the cable car tour. Walking around Ghirardelli chocolate factory is right there near the wharf . . .
There really is so much to do that you really can't go wrong.
have fun.
B.