I guess other people have broken the news to you that you have unrealistic expectations. Please forgive my brutal honesty in advance. I think that you would love living the Bay Area, if you had a comfortable income. But single, nonprofit income for a family of four is not going to be enough to live well here.
It takes about 30 minutes to get in or out of San Francisco during rush hour. You should give up hope of a 30-minute commute, at least if you are talking door-to-door time. I am guessing that you are not used to living somewhere with public transportation. The thing is, an hour siting in traffic every day can be hell, but an hour on a train reading is not so awful. While I know that people do it, personally, I have never heard of someone who commuted to S.F. in a car.
Your best bet is the East Bay. It is served my BART and has some almost affordable areas. You would have to choose between someplace with higher crime rates and a more urban feel (Oakland, Richmond) and someplace further away. I think you would probably be happier with the latter. It would be hell if your husband drove to work every day, but doable if he can take BART. I am thinking Castro Valley or Hayward are possibilities for you. Somewhere like Pittsburg or Antioch have some affordable housing because they have been hit hard by the housing crash.
Canyon is not really a possibility, because houses rarely come on the market and would not be affordable. Orinda was mentioned, but it is for wealthy people, as are Moraga, Lafayette, and Walnut Creek. The parking situation at BART stations is difficult - I am not sure what the likelihood of scoring a spot it. You can check out 511.org for realistic ideas about commute times.
In terms of money, $55,000 for a family of four is just enough to scrape by. This report has some very interesting information about the cost of living in California. I would say that you need to make around $100,000 to feel like you are not just keeping your heads above water. At the nonprofits where I have worked in the Bay Area, only the Executive Director is making anything like that. (You can look up tax information on for nonprofits, which will tell you the salaries of their highest paid employees and give you an idea of the possible salary range.)
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