Hmm... to be honest, $100/night is going to be hard to do. One option I can think of is the Holiday Inn on Van Ness. The location is fairly central, but definitely expect to take a cab everywhere at that point.
fisherman's wharf, you'll get tired of it really fast, esp being from Vancouver.
Funny that as a local, and I'm sure this is probably true with lots of people from the Bay, but I've never been to Alcatraz. That being said, it is probably worth checking out. If anything, you at least will get good views of SF.
While it isn't spectacular, another dinner option would be to get a dinner cruise on the Hornblower Yaught. We did it for a friend's birthday a few years back, and the food was so-so, but the drinks were all you can drink (we bought the option to do so) and it does take you on a tour of the bay if you want good views.
If you're going shopping, skip Stonestown, it is just a regular mall. The downtown area at that SF Galleria near the Metreon seems to be newer.
Oh, Kokkari is a pretty good restaurant.
www.kokkari.com
And how can I not forget, House of Prime Rib. Actually, if you stay at the Holiday Inn on Van Ness, HOPR is just a short walk away. Definitely go there.