You really need to look at the Amtrak schedule and where they go from SD. In general - you can catch any number of trains from SD to LA - and then - perhaps the Coast Starlight from LA to SF, but it's all up to you as to where you might want to stop off, whatever. http://www.amtrak.com/coast-starlight-train

As for accommodations in SD - you might enjoy the Victorian B & B in Heritage Park - next to Old Town - and from old town - you can take the trolley to many places around SD. http://www.heritageparkinn.com/

Take the early Surfliner out of San Diego arriving in Santa Barbara before noon. Your next move from Santa Barbara is the 6234 bus (6:05AM) to San Jose. From San Jose you have the option to go to several cities on the Capitol Corridor trains.
The northbound Coast Starlight arrives in Emereyville rather late so you may not want to use it.
If you get to Sacramento, try to get to the California Railroad Museum in Old Town Sacramento. The capitol grounds are worth a walk too.

You might also enjoy visiting Hearst Castle - by San Simeon/Cambria - on the Coast. http://www.hearstcastle.org/

You could depart from Paso Robles - and google away to find connections over to the coast from there - which is about 30-40 miles away.

Thanks for responses. I found my Amtrak brochure from last summer so now looking at some routes from San.D. Since I have done the coastal route to Santa Barbara I might consider taking Amtrak Capital Corridor to Bakersfield with connecting service up into San Joaquin Valley. This would be entirely new territory for me and need to have some comments if this might be good choice and if so, where to stay for several days sightseeing enroute to San Francisco. Otherwise, I will take the coastal route making one stop north of Santa Barbara. I visited Hearst Castle years ago on the Tauck Tour so would skip on this, but might like to see RED WOODS park again. I was in Yosemite Park with the tour but not sure if I could get there to stay overnight and if there are day trips into the Park. Looking forward to receiving more ideas as I look forward to planning a great trip. Thanks to all the experts!

"I might consider taking Amtrak Capital Corridor to Bakersfield with connecting service up into San Joaquin Valley"

The Capitol Corridor doesn't serve Bakersfield or the San Joaquin Valley. It runs from San Jose through Emeryville - Berkeley - Richmond up to Sacramento and finishes (some schedules) at Auburn.

Even if it did, there are no stop-worthy places in the San Joaquin valley.

On the actual Capitol Corridor - Berkeley, Sacramento and Auburn would be 'worth' stops.

Martinez is the intersection of the San Joaquin line and the Capitol Corridor.
The bus from LAX to Bakersfield takes several hours. Since you have a few extra days, take the SJ to Merced and then take the YARTS bus to Yosemite Valley. I doubt that you can get a reservation in Yosemite, but there are options on the way back at El Portal or Midpines.
From Merced go to Sacramento. Some of the SJ trains go to SAC and others to Martinez. You may get a bus from Stockton to SAC.
My favorite HI Hostel is within walking distance of the station in Sacramento.

tomf: "My favorite HI Hostel is within walking distance of the station in Sacramento."

you haven't been to the Sacramento station in a while I'd guess. It is almost 7 blocks from the hostel to the Amtrak station -- but the mental giants who run the city decided it was a good idea to move the platforms 1,000 feet from the station.

Basically it is now about 10 city blocks from the hostel to the trains. Not convenient or easy w/ luggage.

Also do not think there are that many attractions in the Central Valley (Bakersfield, etc) - outside of getting to Yosemite. It's mostly flat farmland.

And while I haven't been there for a while - do recall there are accommodations close to the Emeryville train station (assuming you are arriving late) - or you should be able to take a taxi from there.

Actually - this webpage provides some info about hotels and that the Emeryville train station seems like a relatively safe location. http://answers.yahoo.com/question/index?qid=20100202111151AAmugNa

After reading above, I'm wondering if I should stick with the coastal Amtrak route like I did previously as I really loved the scenic views. I usually stay 3 nights in places to have enough time visiting small towns, meeting some locals and enjoying areas butI will look at Amtrak routes again as it would be great to visit to Yosemite even for a day trip and be able to connect with transport to nearby overnight stop.

I am looking at hotels in San Diego and will need one in San Francisco for 2 nights at end of my trip. Considering the Sommerset Suites in San Diego which is close enough to center.
Will be watching this board to get as much help as possible. Thank you all so much.

The Sommerset is in Hillcrest - and certainly nice enough. The only negative I could foresee is that it fronts Washington - a fairly busy street - so you might ask how insulated the rooms are on that side of the building, or double check that you have quiet room.

It is within easy walking distance of a number of restaurants and a nice jaunt to the Zoo/Museums in Balboa Park. You could also walk to Little Italy and downtown/Gaslamp and Old Town if you really like to walk - but will have to climb a hill coming back. However, I don't think a cab ride wouldn't be that expensive coming back from those destinations.

While it's not on a trolley line - you can probably use the bus system - but I for one cannot offer much help on the SD bus system. Here is one webpage: http://www.sdmts.com/mtscr/BusRoutes.aspx

In San Francisco - we lived in the Marina and loved the residential area - including restaurants and shopping on Union Street and Chestnut St. There is a cute hotel on Lombard - called the Chelsea Inn - and you can walk to the Marina Green - with a spectacular view of the Golden Gate/SF Bay/Alcatraz - and also have plenty of buses to downtown, which you could also walk to but might want to take a bus back. http://www.chelseamotorinn.com/

And mistakingly posted this under another SD topic - but it was meant for you and restaurants within walking distance in Hillcrest.

Our favorite Mexican restaurant now is Casa Guadalajara in Old Town - http://www.casaguadalajara.com/ and they also have a great happy hour with full/complimentary/hot H' or D'oeuvres and bargain Margaritas.

But in your immediate Hillcrest area - you could go for a month of good dining - and still have some options left, and there are also a number of different cuisines - including Thai. http://www.urbanspoon.com/n/27/2625/San-Diego/Hillcrest-restaurants

One small/authentic "hole in the wall" Mexican place - within walking distance - is El Zarape on Park Ave. Very inexpensive and love their fish tacos.

Here is a review for El Zarape and other restaurants in the area - again - a few blocks from where you will be staying.

http://www.urbanspoon.com/n/27/2674/San-Diego/University-Heights-restaurants

Many thanks to all. Still having problem deciding which route to go north as I want to see best scenic areas. I would appreciate help doing itinerary. Not familiar with Merced, SanJose or some of the stops mentioned above. If I can get on Yarts bus to do day trip to Yosemite and stay in the area for 2 nights I will consider this. Is Yarts Bus a tourist bus that takes visitors into and around the scenic drives in Yosemite? I have a pass for the National Parks so not sure if I can use it in Yosemite. On my earlier visit to Yosemite with Tauck we had a full day and some more enjoying park.

I enjoyed half day at Berkeley on one of my trips and then continued on metro back to Wharf.

Will look at Chelsea Inn to compare rates. Thanks to all for your help and patience.

Taking Amtrak up the San Joaquin Valley is not the most scenic route. Farmland and crummy towns, boring. Merced has nothing to offer other than a jump off to Yosemite. I can't give any info on how the YARTS operates, sorry. For the best scenery, stick to the coastal route.

Everything you need to know about YARTS: http://www.yarts.com/
It's about the only way to get to Yosemite without a rental car.

Assuming you go up the State via the Coastal route - arriving in the SF Bay area - it seems like a lot of work via public transportation to try and get to Yosemite for a night or two.

If it were me - I would just enjoy more time somewhere along the way or in SF.