FYI - Another awesome train ride in the Bay Area
I just happen to read your post about enjoying train rides and considering the train ride in Santa Cruz. Napa Valley is just about an hour north of San Francisco, they have an incredible Wine Train, that includes a couple hour train ride through the Napa Valley. You can also opt to have a snack, lunch or dinner (and of course, the fabulous Napa Valley wines) on the train.
You probably have more than enough suggestions by now, but I just thought I would mention it as another option.