Welcome to the Bay Area. I've made the conscious decision that I'm not willing to pack my family into a 1000 sq.ft. shoebox, which is all that's affordable anywhere near employers, so commute it will be.
Try to make your commute part of your workday? Even if you left at 7am, worked on the train, worked in the office till 4 then home at 6, it would make a big difference to your life.
Source: had a 1.5hr commute in London (bus, tube, train, bus). 1.5 was best case scenario. I will never forget the sheer happiness I gained from changing jobs to a more reasonable commute.