I like where you are going with this idea- I was a bike/bus commuter in Minneapolis for a number of years.
Section 1) Continuous Bike Path There are a number of bike paths built on old trails and railway paths that cut through Minneapolis and connect to surrounding cities. They make commuting via bike much safer and faster than ever before.
It took a long time to get these trails built. The city had pressure from bicycle advocates and it took years of land-use planning. It maybe helpful to read about the history and development of bike paths in the City Bike Master Plan: http://www.ci.minneapolis.mn.us/www/groups/public/@publicworks/documents/webcontent/convert_275983.pdf
I quickly searched to see if SF county has anything similar and found the link below. http://www.sfmta.com/projects-planning/projects/2009-san-francisco-bicycle-plan
Section 2) Bus/Bike designs from Minneapolis - I am a fan. http://www.metrotransit.org/bicycle-racks-on-buses-and-trains