I also recommend The Monk's Kettle
, they pair Belgians (and other beers) with their (really good) food... It also gets crowded, but you can go early evening, put your name on the list and go to one of the many bars in the mission, and they will call you when your table opens. I really recommend it!
About the Toronado... it does get really crazy, and the bartenders can be punks, but if you go early on a week day its pretty awesome.
As far as transportation, SF is actually pretty small, you can rent bikes and get around pretty easily and the public transit system is pretty good.