A few of my thoughts on the beer recomendations:
City Beer is a one stop shop for most of your bottle needs but expect to pay at least a few dollars more per bottle than other places, and it isnt really all that close to anything else beer related, or anything else period. Of course finding a store with that kind of selection in the city is tough. At least it's walking distance from a BART station and parking in that neighborhood isnt bad. I havent been since the anniversary week in May so I can't comment on the tap lineup these days but it was decent before so I can only imagine that it'll be better now. And I think you can buy and open your bottles there.
Beer Revolution will have most of the same stuff for cheaper and have more taps, and it's a block away from Nation's Burger, which is pretty good. Good old greasy American food, with chili available on everything.
While you're in the area you might as well check out the Trappist. It's a cool place but it's very San Francisco, including the $9/pint pricing. So it'll be love it or hate it. They'll have something enjoyable on tap for sure though.
I agree that the barrel warehouse is pretty awesome, and it's not all just barrel aged stuff. They'll always have the regulars on tap (IPA, 1500, Red Eye, etc) and probably a dozen barrel aged offerings. It's right next to the regular brewery, also, about 1 mile from the BART station if you're up for some walking.
If you're into wine bars then Flavor is awesome, but I'm sure you've been there Aliza. I hear they have good food too but honestly I've never eaten there, it's just a place to try some Moonlight beers after leaving Russian River for me.
If you're doing Toronado while in the city you should walk next door and check out Rosamunde. They have some pretty good sausages and since Toronado doesnt serve food you're allowed to bring in whatever you want to eat. As much as I like to talk shit about the terrible service at Toronado their tap prices are good, the juke box has some good music on it, and the bartenders go through phases where they forget they're assholes and act nice. And if you're into $40 bottles of Cable Car, they're always available. While on Haight, buried between the smokeshops, clothing stores, and used record shops there are the mandatory stops: Magnolia and Amoeba, and down the street from Amoeba is the newest SF brewery Social Kitchen, who has good food.
