Not from San Francisco but I've been there several times and it is one of my favorite cities. While 101 is indeed scenic, the Pacific Coast Highway (1) is moreso. I've not been south of Cambria, CA, but the section between Cambria and San Francisco is well worth the extra transit time. A big piece of this section, Cambria to Monterey, is "Big Sur" which has some of the most fantastic coastal scenery I've ever seen.
Once you get to SF, the areas you mentioned are good to see. Well, except just be aware that Fisherman's Wharf is relatively touristy and not particularly authentic. In addition to what you listed, I would suggest just roaming some of San Francisco's neighborhoods. Chinatown is great of course - the Frommer's San Francisco book has a great "self guided tour" of Chinatown. And North Beach is also awesome - a friend and I did the "self guided tour" in the Lonely Planet book. It is also fun to hop in the car and tool around the Presidio and some of the more residential areas around Golden Gate Park.
Finally, if you want a nice day trip out of the city, take the PCH NORTH out of San Francisco into Marin County and up to Point Reyes National Seashore. Beautiful scenery up there, and good hiking if you are so inclined.
Restaurants - I highly recommend Moose's, which is right on Washington Square Park in North Beach (1652 Stockton St). It is "fine dining" but is not too terribly expensive, and is VERY good. The Stinking Rose, an Italian restaurant known for its heavy use of garlic, also in North Beach (325 Columbus Ave), is another favorite. Try the Garlic Prime Rib.
Hotels - there is one place and I cannot recommend it enough. That is the San Remo Hotel.
http://www.sanremohotel.com/ Super clean, neat ambience with books and reading areas throughout, and CHEAP for its location. And the location is fantastic - it is smack dab half way between Fisherman's Wharf and North Beach. You can walk to a lot of the sites I mentioned and are like a block from one of the main cable car lines.
Note the bathrooms are shared in this hotel. Don't let that scare you - they keep the place IMMACULATE. Its cleaner than your house almost certainly. They even have heated towel racks! My friend and I stayed there for 3 nights, in one of the rooms without a sink. I was leery at first but it was fantastic, frankly just like being at home. I really can't recommend this place enough.
Now, if you want a TV, a phone, etc, this isn't the place for you. But if, like my friend and I, you are out most of the day and just want a clean, comfortable place to relax, read, and sleep, that has nice "Old San Francisco" ambiance - its perfect.
Good luck on your trip!