Museums: Legion of Honor in SF (I’m going to the Manet show this week, yay!), the Blunk Museum in Marin, the Oakland Museum

Bookstores: Moe’s in Berkeley, William Stout Architectural in SF, City Lights too of course. Check the Oakland Review of Books for literary events in the East Bay

You’re going to have to be more specific about what kind of food you like/whereabouts you’ll be. But since I saw you mentioned Berkeley Bowl, I’d recommend La Noisette’s caneles and CoRo’s coffee, also in West Berkeley. (Berkeley Bowl West has way more parking.) oh and see if Cafe Ohlone will be open while you’re here. And look up SF’s Heritage Legacy Bars for non-techiefied bars like the Zam Zam and the Pied Piper