Thanks everyone for your helpful replies. I have checked out all the recommendations and they all look ideal...BUT...Our dates have changes to September and the Sunday night in the middle has become really difficult to book, all the hotels mentioned have no availability on the Sunday night. We didnt want to have to move hotels in the middle of our SF stay in the city (Fri- Tue). There is a big convention happening in SF and a baseball match! The only hotel options available were in the '000's per night, not an option, or the apparently seedy end of things, again not an option.
What we have found is an apartment in the Wyndham Canterbury Resort through the 'Flipkey' site which appears to be close enough to Union Square. I did take the recommendation to stay near Union Square. Thanks!
dub_nerd, we dont plan to go to Napa Valley, having lived in Yarra Valley outside Melbourne I think we have enjoyed the 'Cellar Door' experience there.
Again,
Thanks everyone, this site is amazing!