Just catching on to this thread now, sounds like you already have quite the trip planned!
As a SF resident, my personal opinion is that 4 nights is more than enough to see the city and could be worth taking a side trip to Napa/Sonoma since you mentioned that you're interested in staying in cottage-style places. Someone already suggested Meadowood and another favorite is Calsitoga Ranch.
Also, someone also mentioned that the RC Half Moon Bay could be worth a stopover, and even if you don't stay over the Sunday brunch is a delicious way to enjoy the property and especially the view