I would reach out to the the SF Bay Area HU community. See if someone can
help out. Inexpensive accomodation in San Fran is a bit hard to find, but
don't give up. Lots of motorcyclists there. There are some Hostels right in the City. No idea where or what they're called. If you want to camp just north of the City there are a lot of places. (see China Camp, or Point Reyes)
I would avoid the Honda dealer in SF for sure. (Golden Gate cycles) OK for parts but thats all.
For service there are a number of independent shops and mechanics who should be able to handle your AT. I am a bit out of touch with most of them
as I do all my own work and my Vstrom just never breaks.
You are aware that the AT was never imported to the US? So that means most Honda dealers are won't even try to find parts for you. You may
need some help with this.
Common stuff is no problem (chains, sprockets, oil filter, tires, bulbs, electrical (most). But if you bike uses a special air filter that could be tricky. Engine parts might be tough. Someone around here must know sources for your bike. They are very highly regarded and well known, just rare around here.
Subterrranean Cycles (see Pat)
Also, go on Craig's list (san francisco) and ask for help. (motorcycles for sale)
What all does your bike need? Anything serious or just basic maintenance?
Do you have the workshop manual?