I may be missing the point entirely, but is it possible that San Diego to San Francisco (and vice versa) ought to be the limit of the train, no going on from there, just take the train to the barn, clean it and get it ready to head back to the other end of the route? SD to SF is 502 miles, which can be done in less than 10 hours if need be, but it might work best for arrivals/departures in LA and San Jose if they stretch it to 11 hours. The longer the route, the more likely cascading delays will mess with on time arrival. Plus 502 miles fits into the proposed change to the PRIIA 750 mile LD rule, which would become a 500 mile rule instead.
When it comes to sleeper trains in the US, I think that the KISS principle is a good one to follow.
A major problem with that idea is that I don't believe that there is anywhere to store a night train in either San Francisco or San Diego... In the immortal word of Rosanne Rosanadana, "Never mind." LOL!