For once I believe I can help in an accurate and up to date manner, as I am currently sitting in an internet cafe in Siena, and spent yesterday in San Gimignano.

I would ignore the train. I believe the nearest stop may be Poggibonsi anyway, in which case you would be taking the same bus that you need were you coming from Florence by bus (so you would have only the change of buses, not the additional change of trains at Empoli).

Buses From Florence to Siena appear frequent- at least hourly. Similarly the bus timetable I have show buses about every hour from Poggibonsi to SG. From Siena there are some buses that go directly to SG via Poggibonsi without needing to change.

Tim, Hampshire, UK