I assume you don't want to drive? The drive is fast and easy, it should take 2 hours on weekends or in the middle of the day (not morning or evening rush hour).

It looks like you have researched all the other options and costs very nicely. One caution is sometimes the Amtrak trains get delayed so you might take an earlier train than one that will get you to LA just in time. The Flyaway Bus to LAX runs 24 hours.

There is a local train service that uses the same tracks called the Coaster. It goes as far north as Oceanside, then you must transfer to a local Metrolink train. They go all the way to LA Union Station. The only reason I am mentioning this is Coaster/Metrolink has more trains than Amtrak (but makes more stops) and also I don't want you to confuse Amtrak and local trains when buying tickets or boarding.

The left side of the train is more scenic because the first half of the ride is right along the beach in many places. At the San Diego station sit on the side of the train facing away from the station and closest to the cruise ships and harbor. It will be obvious when you are there.

How are you getting down to SAN??