I was not in the San Francisco area when I obtained mine, so can't speak to that. There are a few forums that would likely be much more helpful than this one. Expat forum Portugal, Expat exchange and Anglo info were very useful for me when working on my long term visa. If you google "expats Portugal", you will find lots of things. I'm assuming you have discovered the Portuguese embassy site. That gave me good info also. As I lived more than a two hour drive from Washington D.C., I did all mine by email and snail mail. It took 6-7 months counting the time it took for my FBI check to be returned.
If you want to PM me, I would be happy to answer other questions. The process was a hassle and stressful, but very worth it. I've been here since October and love it!