Well, i definitely can’t help you with the alternaqueer stuff. While i’ve got a few gay friends from SF, and i’ve been to a few parties, i don’t really know the scene at all. The best i could do is point you in the direction of Castro Street and say, “Check out that area.”
San Francisco is a great city for walking, although the hills mean that it can get tiring if you’re not up to it. As alexandra says, Valencia is great, and so is Mission Street, which runs parallel, and this whole area has the advantage of being reasonably flat.
The whole Mission District has great food, interesting people, good bookstores and some really great murals, mainly in the back alleys. I’ve taken a bunch of pictures of them over the past few years (e.g. 1, 2), and if you like this sort of thing i’d be happy to spend some time walking through the Mission with you. It’s always a good place for lunch and/or getting a drink too.
Fried Dough Ho’s museum suggestions are all excellent, and the Legion of Honor also has the advantage of offering great views of the Golden Gate, as well as some great walks out along the cliffs to the ocean.
I think that Alcatraz is worth a visit, if you have a few hours to spare. It is a pretty standard tourist destination, but i think it’s a really interesting place, and you also get the advantage of getting out on the water to get there and back.
If you like sitting in cosy cafes reading, alexandra’s suggestion of North Beach is excellent. There are some great old cafes up there, and my wife and i frequently spend a few hours just relaxing with the newspaper. Especially nice on cool, winter days. You can also walk a bit further and go up to Coit Tower, which has some great views out over the bay and the city, and some really nice WPA murals inside.