orange,
"Walk at Fisherman's Wharf/Embarcadero and walk around that area. Maybe lunch in Chinatown"
You'll def want to walk to/through Chinatown. A zillion food options. I highly recommend Yuet Lee for a cheap but amazingly delicious meal (sweet and sour pork and BBQ pork chow mein are especially great) or maybe dim sum (Great Eastern and City View are two really great dim sum places but you order from a menu, New Asia is a giant one with carts if you prefer that).
"or food trucks (we really want to check out the food truck scene in SF)"
http://offthegridsf.com/markets - tons of SF weekday food truck markets
http://somastreatfoodpark.com/ - a big food truck site
"During the afternoon, I think I would like to rent some bikes and go across the Golden Gate Bridge, followed by driving to Muir Woods."
Biking across the bridge is cool, but I'm not sure about your plan of going there and back, then heading straight back over to Muir Woods. Muir Woods is pretty awesome, though. One thing a lot of people do btw is bike over to Sam's in Tiburon for some food/drink and then take the ferry back.
"Dinner would be either sushi or something of that nature. (Girlfriend doesn't really like raw fish, sadly, so we'd be looking more for places that serve more sushi rolls)."
I would not rec Sushi Ran for someone who is not really into sushi. RBK is right they have lots of other good stuff, but you really way overpay there for someone who is not really into sushi. Also they changed chefs and aren't as good as when RBK was there.
Two great options close to you:
http://ryokos.com/ - more of a party vibe and a huge array of crazy rolls, will be a bit of a wait to get in but nothing crazy
http://www.sfsakana.com/ - more chill traditional place, fewer crazy rolls, but probably more than enough
"Do a wine tour in Sonoma. I've read some good reviews here on Platypus Wine Tours (
http://www.platypustours.com/join-in-wine-tours.php). My girlfriend and I are huge noobs regarding wine quality/knowledge, so any recommendations/advice you guys could give would be nice."
Platypus looks like you have to get to Napa yourself? I would highly recommend a tour like this $99 one
http://www.winecountrytourshuttle.com/ I've done that a couple of times with friends fitting your description, and it's great. You get on a bus at like 8am and then go to a few wineries w/ free or modest tasting fees and reasonably priced wine if you want to buy, then take the Ferry back to SF and arrive back like 430pm. I think that is a million times better than dealing with getting up there yourself, picking wineries, dealing w/ driving, etc.
"After wine tour, I'm thinking we will go to Planet Granite, which is a rock climbing gym in SF."
I'm not a climber, but all my climber friends seem to prefer Mission Cliffs to PG.
"Dinner, I'm looking for mid range restaurant- maybe $50-$100 a head (we don't really drink much, so food quality is more important than drinks). Anything you guys can recommend would be great here as well."
Read the thread for this, lots of suggestions in this price range, and SF is one of the best places in the world for amazing dinners in this range. Feel free to ask re: specific types of restaurants.