There's a whole host of great dojo in the San Francisco area. The Bay Area has probably the highest concentration of aikido dojo in the United States with at least a few dozen dojo within an hour's drive.
The best thing for you to do, I would say, would be to go and visit as many of the dojo as you can at the beginning. It sounds like you have enough experience to ask the right questions and look for the right "stuff" at the dojo. I could give you personal recommendations, but they would be based on my own experience in the art which is undoubtedly different from yours.
Heck -- you could be like me and just dojo hop for a while in the area. I can say that I didn't encounter any dojo there who didn't welcome me in during the time I wandered around...
Good luck! Let us know what you find.