If you can put up with it, I'd recommend doing a short term lease while you get a feel for the city. There are advantages and disadvantages to different parts, and I don't think you'll have a good idea of what's right for you until you've been immersed/found employment, etc. Bring a bicycle and plan on spending some time getting acquainted with the city.

Something like Lower Haight, SOMA, or Duboce Triangle area is centrally located and would be a good starting point to explore.

I will second Duboce Triangle, I live in this area and find that it has excellent bus and train routes to just about everywhere in the city.

Congrats on the move, Paul, and good luck in San Francisco!

Be prepared that SF != Silicon Valley. Different culture, different companies, 1 hour+ commute or so each way.

To be honest I used both terms in the title for SEO purposes.