I realise I'm a little late to the party here... but some of us have to spend time traveling on the train!

If you're just trying to get between Salinas and San Francisco, Monterrey-Salinas Transit has a bus the goes to San Jose, where you could catch Caltrain. I'm not familiar with the schedule, equipment, or cost, but it appears you'd have to connect in Prunedale.

As for Diridon Station... Even during commute, it shouldn't take much more than five minutes to walk from the furthest bus bay, through the station, to the light rail stop on the beyond the tracks. Amtrak's buses all stop closest to the station.

If you want to go the all Amtrak route, I'd suggest booking the bus between Emeryville and San Francisco. It's a guaranteed connection and virtually free when booked with your train travel. There's nothing wrong with catching BART at Oakland Colliseum or Richmond; but it's neither guaranteed nor timed.