What I'm thinking is that you could do a figure 8 loop. Do a south of SF loop for a week, followed by a north bay loop for the second week. The south bay loop may not be as interesting as the north bay loop but that's just my prejudiced opinion, being a north bay guy.
Here's a suggested North Bay loop. Get out the map.
SF via Ferry to (or coming out of the south bay loop) Vallejo, ride up 29 (and some other roads) to Napa. Vallejo to Napa will suck but there's no other really good way to do that (unless someone has suggestions).
Napa to Calistoga via Silverado Trail and some other side roads. For side roads consider going out to Chiles and Pope Valley and come back over the hill into St. Helena. Calistoga then is a likely overnight.
Continue north of Calistoga on CA 128 to Jimtown thence to Healdsburg. Or on up to Geyserville and then come back to Healdsburg.
Consider staying in Healdsburg for two nights, using the next day to do some loops in the area, or join the local bike club, www.srcc.com
for some local flavor. Moseying around Dry Creek Valley is pretty sweet and there are some great Zins in the neighborhood. If you like beer, Bear Republic Brewing is there and well worth the stop.
Couple of options from Healdsburg:
1) Ride Westside Road to Guerneville. Don't take Sweetwater Springs unless you like climbing. Ride to Bodega Bay. consider two nights in Bodega Bay so you can ride to Occidental, Valley ford, Freestone before continuing on back to SF. Don't miss the bakeries in Tomales and Freestone - seriously - look for the bikes.
2) Ride to Sebastopol then up to Occidental (Graton Rd. or Occidental Rd. either one works, Graton rd is preferred). Stay in Occidental. Again consider staying 2 nights in Occi and do the Coleman Valley loop to Bodega Bay -> Bodega -> Freestone -> back to Occidental. Next day, Occidental -> Freestone -> Valley Ford -> Tomales -> Pt. Reyes Station -> SF. There are more steep climbs on this route, and don't take CA 1 from Valley Ford to Tomales, even though it is the ACA route. Lots of traffic, narrow road with no shoulder and steep climbs. Locals don't ride this stretch and neither should you. Take either Franklin School Rd or Whittaker Bluff. Both have steep stretches but zero traffic and great views.
3) Ride directly out to the coast on Skaggs Springs to Stewarts Point. Skaggs is hors de categorie (sp?) in steepness and nasty climbs but spectacular. If you're heavily loaded I would skip this. Lodging is a good guess and I can't offer any suggestions. However CA 1 south has some great scenery and wicked climbs. After you reach Bodega Bay you would continue as described in option 1.
I don't have a good south bay loop, but thinking out loud, the thought that goes through my mind is something like this: SF -> Santa Cruz, Santa Cruz around through Watsonville ->Morgan Hill -> San Jose; over Mt Hamilton and on to the Mines Road to Livermore; Livermore up through the San Ramon Valley to Martinez (or Crockett?); cross the Carquinez Strait (bike routes on both the Carquinez and the Benicia Bridges) and make your way over to Vallejo to pick up the route above.
Give that some thought and let me know what you think.
Santa Rosa, CA