You're hitting my area of California for this trip.
SF: Anchor Brewing - A great historical brewery with brews you can't get anywhere but there.
Ripon/Manteca: Kelly Brothers - Ask lots of questions and tell them your a homebrewer. They'll give you extra special attention! The Four Towers IPA is pretty good.
Stockton (If you get there) Valley Brewing. Try the burger and yam fries with their house IPA. I used to go here once a week when I worked in Stockton.
When you're in the Napa area visit Russian River Brewery in Santa Rosa. They won't have any Pliny the Younger on tap anymore, but they have some of the best beer on tap that your tongue will ever taste! Consecration is a must as well as their Valentine's beer Rejection. Pliny the Elder on tap is also something you have to do once in your life.
One word of advice in the Napa area. The cops are everywhere and they have a zero tolerance policy for drunk driving. Have a designated driver for sure!
Let us know where you went and what you liked best when you get back.