Take the Ferry to Sausalito and go to
Sushi-Ran. Ichi Sushi in SF is well-known, just moved. I have a long list of favorite restaurants in SF (most of whom carry our wine): Frances, Salt House, Quince, Perbacco, Cotagna, Anchor & Hope, RN74, Spruce, Farallon, Benu, A16, La Folie, Michael Mina, Piperade, Saison, Coi, etc. -> let me know what food you like and I'll guide you.
As to where to stay, depends on what kind of neighborhood you want to wake up in. Most of the more interesting ones don't have hotels. Lots of touristy stuff to avoid in SF.