I visited San Francisco for the first time over this most recent summer on vacation and got my best advice from a friend who works in the area- he suggested visiting co-working spaces or "entrepreneur" popular coffee shops as the best way to make connections or network outside of getting a introduction from a friend of a friend.
The list of locations he suggested to me are the following:
Coworking:
http://wiki.coworking.com/w/page/16583935/SanFranciscoCowork...
Coffee:
Fourbarrel Coffee: http://fourbarrelcoffee.com
Coupa Cafe in Palo Alto: http://www.coupacafe.com/
Coupa Cafe on the Stanford Campus: http://www.coupacafe.com/locations/stanford-green-library/
The Summit: http://www.thesummit-sf.com/
It is quite awkward to just "drop in" and cold visit these places, but I found that attending during an event made for a perfect occasion to network.
Also, have you tried just reaching out to any startups you are interested in? I was able to visit several just by contacting them ahead of time (important), explaining what I wanted clearly (introduction, advice, etc) and then setting up a lunch or tour.
