SF doesn't have "centuries" of infrastructure. The great earthquake and fire in 1906 destroyed nearly everything. SF doesn't have "vastly limited space" either. It's not even in the top 100 cities in the world in terms of population density. Source: http://www.citymayors.com/statistics/largest-cities-density-...

Nor are SF's roads and bridges really all that complex. Pittsburgh, Pennsylvania, has 446 bridges, and is one of the cheapest cities to live in in the United States. Maintaining two big bridges just isn't that complex, certainly not enough to explain a 10x factor in the cost of living. Sure, SF has a high minimum wage for construction employees, but so does California in general. And somehow it is not that expensive to live in Fresno or Sacramento.

If anything, rural and suburban areas tend to have to maintain more infrastructure per taxpayer, since people are more spread out.

Nimbys are strong in SF and prevent building up. Tokyo, which has a similar earthquake problem has built up.

Not really. Japan's "sunlight laws" make it really hard to go above around three stories or so, meaning that nearly all of Tokyo's skyscrapers are concentrated in a few hot spots with commercial zoning (Shinjuku, Marunouchi) plus a few mega-developments like Roppongi Hills where the developer could pull enough strings to buy a large chunk of land and bulldoze their way to an exception.

Of course, compared to Silicon Valley, even the suburbs of Tokyo are indeed densely packed -- but then, Tokyo also crams in something on the order of 7x more people into the same area.