1. You can connect to the Surfliner directly from the Starlight at Los Angeles. It was a guaranteed connection last time I looked (assuming it is on the same reservation number). There are a couple downsides to this. It is the last southbound Surfliner of the day and gets to San Diego a bit after 1 am. If the Starlight is too late to make it, the guarantee is protected using the night bus that leaves LA at 2:25 am and gets to San Diego at 5:25 am. A popular alternative is to take the Starlight to Santa Barbara, a beautiful coastal town wedged between the Coast Range mountains and the Pacific with lots of amenities, stay overnight there, then take a Surfliner through to San Diego the next day. There are 5 trains a day between Santa Barbara and San Diego.
2. Just so you know, the southbound Starlight makes a pretty clean miss of mountain viewing. Crossing the Cascades in Oregon is in the evening and most of it is after dark much of the year. You will get at least some of the coast running that is very roughly between a bit south of San Luis Obispo and a bit north of Oxnard unless the train is very late. Northbound both the coastal running and the Cascades are mid-morning.
3. When it comes to Amtrak, most travel agents are worse than useless unless they are rail travel specialists. Most here book direct with Amtrak, either by phone with an agent or the web. Amtrak agents are quite helpful. I understand you may be able book by chat with an Amtrak agent now, too. The only rail travel specialist travel agent I knew died, btw.
Also, avoid Amtrak Vacations, an independent third party travel agency that licenses the name and does joint marketing with Amtrak. They have a poor reputation for customer service, have worse cancellation and refund policies than Amtrak itself and seem to overcharge for mediocre hotels.
Finally, a major rule for successful North American rail travel is never book a same day connection to another carrier from any North American long distance train (Amtrak or VIA).
