Not sure you can avoid Amtrak the whole way but you could take CalTrain down as far south as you need. Looks like as far as Gilroy (http://www.caltrain.com/caltrain_stations.html)

Then you'd probably have to catch Amtrak from there. At least it's only half a pain the ***?? Or.. hmm.. you could probably ride from Gilroy if you spend the night there and take off early in the morning.

http://www.sfbike.org/download/tubet...article05.html