I'm headed to San Jose this weekend with my DD, we are going to head to the Tech Museum and to the Rosicrucian Museum. If there is no snow over the Sierras. I grew up in San Jose and we go a couple of times a year. We have spent about 11 days in SFO this year also. We love the city.
If it were me, I would attend the conference in San Jose and have a car there if you are planning on sight seeing etc. while in San Jose. A nice drive to Big Basin Redwoods State Park
http://www.bigbasin.org/to see some redwoods, or perhaps out to Santa Cruz
http://www.explorer1.com/santacruz/attractions.htmfor dinner on the wharf or even just to catch an amazing sunset on West. Cliff Drive.
In SFO, ditch the car. Use Muni, cabs, BART and cable cars. Parking in SFO is spendy, plan on $25-35 per day and that includes at most hotels.
My favorite place to stay is a bit off of the beaten path, in the somewhat quieter community of Cow Hollow/Marina Dist. I like the Travellodge Golden Gate on Lombard and Steiner. Not fancy by any means, but it is clean, very reasonably prices and close to shops, restaurants and Muni stops. It does have free parking as a perk. We usually arrive, park and never take the car out until we depart. We don't visit the city to go shopping so Union Sq. is not a draw for us. If you like shopping, a lot of shopping, then staying in Union Sq. would IMO be very desirable.
What not to miss really depends on your tastes. For me it would be a walking tour of the Golden Gate Bridge via City Guides (free tours)
http://www.sfcityguides.org/
I also love china town, I love the sights, smells and restaurants as well as the atmosphere and if you are really adventurous, get off of Grant St. which is the main "tourist" drag, go up a block to Stockton and explore the local markets. The fish/poultry markets are incredible to see. SFO has super strict health codes, it is safe to eat anywhere, you may not like it but it won't harm you so give it a try. Our favorite restaurant is the Washington St. Bakery and Restaurant on Washington Street just below Grant St.
http://www.washingtonbakerysf.com/
Cable car riding IMO is a must, I like the California line, far less crowded with tourists and it goes up and over Nob Hill, past beautiful hotels (Mark Hopkins and the Fairmont I believe) as well as Grace Cathedral on the corner of Taylor St and many beautiful homes.
http://www.sfcablecar.com/routes.html
We always buy a Muni pass that is good for unlimited use of buses, trolleys and cable cars. FYI a muni pass is not good on BART, that is a separate entity.
The "Impressionist: Masterpieces from the Musee D'Orsay" currently on display at the DeYoung Museum is really beautiful and IMO worth the visit, we saw the first phase in July and will be returning in January to see the second phase.
http://deyoung.famsf.org/
The newly remodeled Calif. Academy of Sciences is amazing.
http://www.calacademy.org/
Coit Tower and Lombard Sr. would also be on my list of things to do. I think City Guides does tours of both, check their website for more details.
Then of course there is the tourist mecca of Fishermans Wharf which IMO is worth skipping, but if you have never been you might want to swing on by, have a clam chowder bread bowl so you can say you did and say hi to the sea lions.
http://www.fishermanswharf.org/
Something else I would not miss would be an Alcatraz tour and I highly suggest you try for the one that is at night! Its amazing. Book in advance, these sell out quickly
http://www.alcatrazcruises.com/
The Walt Disney Family Museum is really quite an extensive collection and I suggest you allow at least 4 hours. We really enjoyed the history that was there and learning the story of who Walt the man himself really was.
http://disney.go.com/disneyatoz/familymuseum/index.html
Almost forgot, since you said you like History, a visit to Ft. Point might be worth your while.
http://www.nps.gov/fopo/
Also refer to Yelp.com for great neighborhood restaurant reviews.
I would stay in SFO for the first leg of your trip and I would take a shuttle/cab to the hotel from the airport since you are arriving late.
If you get a car on Thursday, you could meander down Hwy 1 from the Golden Gate to Santa Cruz then cut inland to San Jose via Hwy 17 (880) or take the scenic Route Hwy 9 from Santa Cruz, and head to Big Basin - Goggle it, this is memory based and it has been many years since I went out Hwy 9 and even more years since I was at Big Basin.
If you are flying out of SFO you can return the car to the same place you got it and not pay what can be huge destination fee's.
November can be a great time of the year weather wise, the fog is not as prevelant as it is in the summer.
If you are set on not getting a car, there are ways around it but it would make the outlying destinations like the redwoods hard to get to unless you took some sort of tour. There are tours that go North from SFO to Muir Woods but I don't know anything about them. We drove up there last spring in our car.
If you opt out of a car, do a bit of research on getting to the South Bay from the North Bay and visversa. I am thinking it would be best to take BART to one of the Train stations and then take the train into San Jose. My Brother used to commute from San Jose to San Bruno via train on a daily basis so I know it is very possible if not easy, I'm just not familiar with it. Perhaps the hotel in San Jose could help you with that one. I also know that BART does go to the airport. Depening on how late you get in and where your hotel is in SFO BART could also be an option for getting to your hotel.
San Jose,
Comfort food:
Harrys Hofbrau
http://www.harryshofbrau.com/