Hello again. I promised I'd report back as to how it went.

Splendidly, thanks to all of you. In the end, this is what I did:

Booked a multi-city trip departing San Francisco Ferry building on the 08:20 Thruway getting off at Salinas at 10:50 (I think this Thruway is intended to connect to the Pacific Surfliner.) For the return portion I booked Salinas-Santa Clara Great America departing Salinas 15:30 and arriving San Jose 16:50 ostensibly to connect to a Capital corridor train leaving around 18:00. This involves a Thruway bus to San Jose and technically a hookup with the Capital Corridor train to Great America. The Capital corridor is the part I 'threw away.' (Actually when I picked up the tix at the Ferry Building in SF the counter agent guessed exactly what I was going to do and, after verifying that I wasn't actually going to Great America but was jumping ship in San Jose, 'collected' the train portion of the ticket in advance. Apparently this is how Amtrak can prove they sold a train ticket and also helps with their revenue collection in some way.)

Luggage was as I expected: stuck the bigger bag under the bus, took the small one on board. The bus was newish and comfortable, with even an onboard lav and also space with tracks for wheelchair clients to use.)

The bus to Salinas from SF actually arrived slightly early (10:45) and I then took a local city bus (number 43) to Memorial Hospital from where I then walked to the Hertz rental outlet on Abbott St. (They would have picked me up but this was just as fast, plus I got a bit of familiarity with Salinas this way. It is only a very short walk from Amtrak to the Salinas Transit center for local Monterey-Salinas transit buses. Note that as long as luggage is clear of the aisles, one can take it aboard these buses, so I suggest packing light and riding in the off-peak hours.)

Anyway.....

On the return, the bus left Salinas on time and arrived at San Jose slightly early (around 16:30). It was a breeze to walk to the train station where I bought a ticket ($5.75 from the machine) on Caltrain to Millbrae. I actually made it in time to get a 'baby bullet' train that is more or less an express train to SF with very few stops, including ones at Palo Alto and at Millbrae, which is an 'intermodal' station with a platform transfer between BART and Caltrain.

Either way, it was a heckuva lot faster and simpler than taking the Coast Starlight train for the same or similar itinerary.

At Millbrae I have a couple of tips:

It is possible to walk to the Marriott airport hotel (or the Westin, or the Bay Landing, if desired) from the Millbrae Caltrain station. You will need about 20 minutes. If trying to catch a train, don't forget to allow time to exit the hotel (it can be a long hike from your room to the front door) and to buy the tickets from the machine once you get to the Millbrae station. From the Marriott, this means about a journey of 25 mins duration at the fastest - 30 mins is more comfortable.

Alternatively: buy a $1.50 Millbrae-SFO ticket on BART (Millbrae as I said is an intermodal BART-Caltrain station.) This now involves an absurd connection at San Bruno. Yes, this means heading out on BART in the direction of SF, going one stop, then crossing the platform and heading on BART in the opposite direction to that which you just came, i.e. taking an SFO bound train. At SFO, you take the airtrain from the BART station to any terminal (I picked terminal 3), where you alight and head to the courtesy hotel shuttles. From the Caltrain station to the Marriott airport hotel via this route takes ten minutes or so longer than walking (!), but you do get to stay out of the elements, and to sit instead of walk for most of the way. Note also that one or two times a day during the weekdays, there are free shuttles directly from Millbrae to the hotels, but the schedule rarely seems to be convenient so I didn't bother.

Okay, that was a long way to saying: everything went fine, thank you all.