I'm fairly ignorant about the specifics of northern California, but I did persuade my dad to ride the train from Seattle down to Emeryville and then to Denver. I don't remember how long the layover was in Emeryville, but it was a long time for an old man in his 80s. So with that intro, here's a few thoughts:

First, unless you're a speedy long-distance rider, you might consider leaving a bit earlier in the year. I'd suggest a late August trip west, and start back right after Labor Day for more sunlight and less snow as you cross the Rockies.

Second, could you ask your son to come pick you up in Davis, Martinez, or Emeryville? That'd be a few hours out of his day, with perhaps a stop for a meal and/or a few vineyards on the way home. It'd be a relaxing way to end a couple days on the train.

Third, and like the second, could he drop you off when you're ready to head east? I've read some horror stories about Sonoma and Napa valley roads, and close to harvest season might not be the time to tackle high traffic roads with no shoulders. You could pick a point from the Western Express maps that isn't too far from son's house and puts you directly en route.