1) which area of San Fran would clubs (night clubs) be likely to be located in?
All of them. Well, that's not true, but there are a lot of areas of San Francisco with nightclubs. The Marina, Northbeach, and Down Town all come to mind.
2) which is an area where the poorer people live (one of the characters is unemployed, where would he be likely to live?)
South San Francisco.
3) which is an area that you would NEVER walk through after dark, even if someone PAID you, because chances are you would get mugged. And re-mugged. And maybe mugged some more. Like rough neighborhoods are what I'm after.
I'm seconding the Tenderloin, but also some parts of the embarcadero, especially near the Greyhound station.
4) which is a more suburban-y place where you see nice houses with four floors and an attic, and a nice front yard, and driveway and all. I'm hoping for somewhere slightly secluded, too. Don't worry about the price range--the characters are rich, they can afford it
Pacific Heights
5) a nice coffee shop that most people would know and go to (and please not $tarbucks. Please)
Not a clue, though Borderlands would work if you want to go meta. They're a coffeeshop, but mostly a Scifi/fantasy bookstore.
6) a mall or shopping area located close to the place where the poorer people live (I know, why would someone build a mall near people who don't have the cash to buy stuff? But just close-ish would be good enough. Maybe biking distance?)
San Francisco doesn't really have Malls in my experience. It's too Urban for that. If you're willing to have your characters travel, then definitely Hilltop Mall over by Richmond. If you're staying local... I don't know.
7) and, not really a location question, more of a culture question--is Wiccan/magic type of stuff widely accepted in San Francisco?
... No. It's not unaccepted, but, I'd argue that it's not more accepted in SF than it is anywhere else in California.
As a Berkeley native, I actually want to disagree with the Bay Area consisting of way more than San Fran. The Bay Area certainly does, but we're really not that much like NYC. The San Francisco Bay Area and the city of SF are quite different, especially in terms of microcosms. Unless you plan for your characters to be spending quite a long time commuting (Traffic is lethal, and parking is impossible) then spreading your story out too far may cause problems. SF has everything you seem to be looking for, without needing to throw yourself across the Bay Area. As much as we're one unified place, we're not really very unified.
At the end of the day, most Bay Area people don't go into the City except when they're
going into the city. It's not a big deal, but it's also not a nightly thing. Every major area (Berkeley, Oakland, SF, Marin [well, maybe]) has their own cultural stuff, their own food, and their own events. There's a lot of crossover, but not nearly as much as New York City has. We're a lot more spread out than NYC, too.