For the Thruway busses in San Francisco it does not matter where you get on the bus, the ticket will be accepted at any stop within the City of San Francisco, I know this from experience usually getting a ticket to the Ferry Building (Embarcadero) but almost always getting on at either the San Francisco Shopping Center (5th and Market St.) or the CalTrain Station at 4th and King.
I'm hoping we can just get on the bus by showing our tickets no matter which stop we chose to leave from. Could it be that easy??
Answer in a nutshell yes it is that easy. B)
As for the leaving the luggage at the Ferry Building stop, in the past this might have been possible however, currently that station is closed due to flooding in the building with an unknown date for reopening. The advisory is located on the webpage for the Capitol Corridor a service of Amtrak California and can be found
here. while Amtrak California is not Amtrak per se they use the same stations namely the Ferry Building. Thus the baggage check would be at Emeryville and would most likely not be able to be done in San Francisco.
If you need any ideas as to where to keep the luggage during that day in SF I'm sure I can brainstorm something.
San Francisco Ticket Office Temporarily Closed
Due to interior flooding at the San Francisco Ticket Office (SFC, Ferry Building Annex), the facility will be closed for repairs beginning Dec. 18th. Although the facilities are closed, Amtrak Capitol Corridor Motorcoach operations are not affected. Passengers can take regular scheduled service to Emeryville and Oakland and be ticketed, as well as check baggage. There is no set date to re-open the facility yet. An update will be issued as soon as possible. Thank you for your cooperation and patience.