score:7
Amtrak does not allow stopovers, but they do have a multi-city option on their web site, and if you book one ticket of multiple legs it may be intelligent enough to do better than adding up one-way fares. If you don't book a sleeper berth, the fare is not that high; Los Angeles to Emeryville as low as $50 if booked far in advance. (Note discount tickets may not be refundable.) Also, this train is 100% reserved seats, and may sell out.