Heck, as no one has piped in yet... I'll tell you the little that I know, although you will later be better served by someone with more knowledge.

All activity is under the cover of darkness unless there is an unusual situation, like an outlaw.

The MBARSDG and the MSDGBAR are the main freight traffic. I believe the northbound tends to leave San Diego around 9 or 10 PM. The southbound is usually on its way from Corona about 6 PM. (In both cases, these are random observations - again, others may know better).

There is an indie outfit (I think Pacific Sun) with some neatly painted GEEPs running the local business. They are also nocturnal, and I have only personally seen the power at Stuart Mesa.

Not sure about any additional auto train movements, but if they do occur, I'm sure that they would be nocturnal.

San Diego & Imperial Valley is also completely nocturnal.