I think you've got most of my recommendations covered. I stayed at the Union Square area and loved it. There was a great little improv club across the street from my hotel. It was several years ago, so not sure if it's still around, but there are lots of cool little places in that area. Actually, it is still around!
http://secretimprov.com
Alcatraz was an interesting tour and it looks like you've already got it booked which is good because I think you need to book well ahead.
We took a "wine train" tour in Napa Valley. It was an old fashioned train that has been restored and it goes to several vineyards in the are. They had a number of different tours. We took one where you got off at one of the vineyards for a tour and then got back on the train on the way back, but some people stayed on and saw more vineyards along the way.
http://winetrain.com
If you like chocolate and ice cream, go to Ghirardellis (near Fisherman's Wharf) for a sundae. My aunt (who grew up in San Francisco) recommended it. I wouldn't have normally gone somewhere just for ice cream but it really was amazing.
We went in July and it was COLD! I knew it was cooler and planned to take a sweater, but it was even colder than I expected. Fall is supposed to be nicer though, so going later in August, I'm not sure if you will get summer weather or fall weather.
We also went to Top of the Mark, near our hotel. We went for martinis, which they are known for, but it looks like they have food there too.
We also did an evening walking ghost tour of the Union Square area. Lombard Street was another interesting walk we did (that was on our own, not a tour).
Loved San Francisco! Enjoy!