Here you go:
It's a long day, but covers most of the great road riding in the area. you will hit:
1) Alice's Restaurant in La Honda for breakfast
2) The Pacific Coast Highway south of the city
3) The Golden Gate Bridge
4) The Pacific Coast Highway north of the city
5) Olema or Petaluma for lunch
6) Sonoma wine country (no sampling!)
7) Napa wine country for dinner
8) A quick highway shot home at the end of a long day
9) The Bay Bridge
And, of course, twisties, vistas, and great towns all over. Feel free to PM me for places to stay/eat/do.
And now that I'm noticing you have 2 days, it would be better to split this ride up south side 1 day and north side the other. If the timing is right and you want company, I could even tag along. I ride a 1200GS and wouldn't have a problem keeping up.
Welcome to the Bay Area!