There is one incomprehensibly lame thing about this Amtrak route. Since Amtrak leases the rail from some freight lines, the freight trains have the right of way. This means that twice the train got stuck between freight trains moving really slowly. So I ended up in San Jose about 45 minutes late, which means I missed the connecting train I was intending to take.
As a result I ended up in at the cal train station at 0:30, and was wandering my way to the hostel at about 1:30 (am), which was, shall we say, slightly creepy.