I haven't been to SF in years, but I'll comment on a few of the shops Rebecca mentioned.
Grooves is run by Ray Anderson who did the Holy See light show back in the '60s, one of the lesser-known light shows but they're on some posters. He knew everybody in the scene at that time in mid-late '60s San Francisco and probably has some fine posters for sale. He has great records but his shop can be hit-or-miss.
http://www.yelp.com/biz/grooves-inspiralled-vinyl-san-francisco
The 45 shop in San Francisco is Rooky Ricardos, on Haight St. near Fillmore, been there for 20 years, mostly soul music.
http://www.yelp.com/biz/rooky-ricardos-records-san-francisco
A few blocks away is Jack's Record Cellar, which someone recently told me was closed but I'm not sure if that's true. If it's open it's worth checking out only because it's an ancient record shop, and it's where Roy Loney used to work, or may still for all I know. Ask for garage and maybe, just maybe they'll pull something out from behind the counter.
http://www.yelp.com/biz/jacks-record-cellar-san-francisco
Also nearby is Groove Merchant which was a big deal once in the funk/soul/jazz world and may turn up something:
http://www.fogworld.com/gm/
Recycled on Haight was always a fun shop that would price decent VG records quite cheaply. Your best bet may be the ugly Amoeba further up on Haight, which once was a classic bowling alley but is now a concrete box. They get the largest quantity of records of any shop in SF and may be the only one that isn't completely picked over when you're looking.
Have fun, wish I was going!
Also, I have a friend in the Mission who deals records, I don't know if he has any garage right now but I can see if he's available.
In the Mission there's Dijital Fix, mostly for LPs:
http://www.yelp.com/biz/dijital-fix-san-francisco