You're very brave to tackle this project. To do it right you'll need to create a lot of custom objects to simulate 1940s era U.S. buildings.
Also, the area has seen massive development over the last 70 years. To depict 1940s SF properly, you'll need to ignore modern STRM data and satellite images and work from old maps. The good news is that a whole lot of the Bay Are which is now suburbs, strip malls and generic office parks was fruit orchards, woods and fields before the post-war mass migrations to the U.S. West coast. That means a heck of a lot less populating to do and a much more frame-rate friendly map.
Fortunately, the USGS has all sorts of historical maps to help you out:
http://bard.wr.usgs.gov/histMapIndex15.htmlCity
No skyscrapers in the 1940s! SF got hammered by the 1906 earthquake and fire and didn't really recover until the 1920s. Most buildings from the period are red brick or beige stucco flat-topped 2-4 story buildings, with some 6-7 story buildings in the central business district. In older areas not destroyed in 1906, there were narrow 1890s style Victorian houses.
The big landmarks in SF during the 40s would be Coit Tower on Telegraph Hill (also a landmark), the Embarcadero ferry terminal at the base of the Oakland Bay Bridge, the Presidio Army Base, Treasure Island Navy Base, Yerba Buena Island, the docks along what is now called Fisherman's Wharf (then a working port rather than a tourist attraction), Alcatraz Island/Alcatraz Federal Prison in the middle of SF Bay and, of course, the bridges. Lesser landmarks would be the parks, museums, the SF Zoo, U.S. Mint, City Hall, and the old U.S. Post Office which have remained basically unchanged since they were created.
In Oakland and Berkeley, developers built lots of "little houses made of ticky tacky" during the 1920s and 30s. These represent yet another sort of house you'd need to model. There was development far up into the Berkeley and Oakland hills, but this sprawl didn't really spill over into the inland valleys until after World War 2.
The Berkeley skyline would be dominated by the University of California - Berkeley campus, although it wasn't as big as it is today. There was also a small army base - Camp Ashby - down by the waterfront.
http://en.wikipedia.org/wiki/Berkeley,_Californiahttp://wikimapia.org/5033334/Camp-Ashby-siteOakland would be dominated by Jack London Square, the Ferry Terminal, the Tribune Tower, City Hall and Lake Merritt.
http://en.wikipedia.org/wiki/Oakland,_CaliforniaRichmond was a major shipbuilding center during World War II
http://en.wikipedia.org/wiki/Richmond,_CaliforniaPalo Alto - mostly rural and light residential, except for the Stanford University campus and a major railroad yard.
http://en.wikipedia.org/wiki/Palo_altoLots of good info and pictures here:
http://www.sfmuseum.org/Bridges
Oakland Bay Bridge - Opened in 1936, massively redesigned and rebuilt in the 1990s following the Loma Prieta Earthquake.
http://baybridgeinfo.org/historyhttp://en.wikipedia.org/wiki/San_Francisco_%E2%80%93_Oakland_Bay_BridgeHayward-San Mateo Bridge AKA San Francisco Bay Toll-Bridge - The original span was built in 1929 and not replaced until 1967. You could probably get away with using standard IL2 bridge objects to simulate this one.
http://en.wikipedia.org/wiki/San_Mateo_%E2%80%93_Hayward_BridgeDumbarton Bridge - Built in 1927 as a drawbridge, later replaced by the modern bridge. Possibly another bridge which could be created using stock IL2 objects.
http://en.wikipedia.org/wiki/Dumbarton_Bridge_%28California%29Richmond-San Rafael Bridge - Didn't exist until the 1960s. Before then there was a ferry service.
Military Bases - During and after WW2, San Francisco was a major military center, with three major naval bases and two big army bases. The big ones are The Presidio, Oakland Army Base, Alameda Naval Air Station, Treasure Island Navy Base and the San Francisco Naval Shipyard at Hunter's Point. A bit farther afield, there was the Mare Island Naval Repair Center along with a number of lesser facilities.
General historical info here, including some excellent maps showing the general location of all WW2-era military facilities in California:
http://www.militarymuseum.org/HistoryWWII.htmlArmy Bases
The Presidio - At the base of the SF side of the Golden Gate Bridge. Harbor battery fortifications dating from the middle of the 19th century. HQ for the Western Defense Command during WW2, among other things. This is still a major SF landmark although the army closed the base and sold off the land in the 1980s.
http://en.wikipedia.org/wiki/Presidio_of_San_FranciscoOakland Army Base - Major embarkation point for troops shipped overseas. Major hospital on base for wounded troops returned from overseas. Shut down in the 1990s.
http://www.militarymuseum.org/OaklandArmyBase.htmlOther army facilities: Hydle, Benicia Arsenal, Staneman, Clayton, Ashby, Oakland, Freemont, Baker, Cronkhite, Barry, McDowell, Mason, Scott, Letterman, Miley, Funston.
USN Facilities
Treasure Island - Artificial island near Yerba Buena Island and the Oakland Bay Bridge. Former site of the 1940 World's Fair, taken over by the USN in 1941. Major embarkation point for seamen going overseas.
http://en.wikipedia.org/wiki/Treasure_Island_%28California%29Hunter's Point/San Francisco Naval Shipyard
http://en.wikipedia.org/wiki/San_Francisco_Naval_ShipyardAlameda Air Station - A joint army/navy base.
http://en.wikipedia.org/wiki/Alameda_Naval_Air_Stationhttp://www.alamedanavalairmuseum.org/Moffat Naval Air Station - In Sunnyvale. Former home to the airship USS Macon.
http://en.wikipedia.org/wiki/Moffett_Federal_AirfieldOther Naval facilities: San Bruno, Oakland, Concord, Tiburon, Cotati, Port Chicago, Santa Rosa, Livermore, Shoemaker and Parks.
USAAF Airfields - There were a dozen or more airfields scattered around the Bay Area. The Airfields database web site is excellent for giving coordinates and maps for all airfields from this period.
http://en.wikipedia.org/wiki/California_World_War_II_Army_Airfieldshttp://www.airfieldsdatabase.com/WW2/WW2.htmhttp://www.airfields-freeman.com/CA/Airfields_CA.htmFairfield-Suisun Army Air Base AKA Travis AFB - in Sonoma. Started in 1942, originally a USAAF/USN facility, later turned over to the US ATC.
http://en.wikipedia.org/wiki/Travis_Air_Force_BaseHamilton AAF
http://www.militarymuseum.org/HamiltonAFB.htmlOther airfields: Crissy, Hayward, San Jose, Concord
Finally, there were a number of civil airfields and seaplane bases which were taken over by the military or the ATC during WW2. A list of modern airports is here:
http://en.wikipedia.org/wiki/List_of_airports_in_the_San_Francisco_Bay_Area