I was recently in San Francisco:
For seafood I enjoyed Swan Oyster Depot (Polk street, check it out on Yelp). When I was there I walked all over. In one afternoon I walked all over downtown (8 miles). I did go down to Fisherman's Wharf but stayed away from restaurants and street vendors. It is fine to see but it is quite commercial. I guess it depends on you. Also ate at Red Crawfish and Sushi Toni and enjoyed both. Though you can find many great places.
Also FYI. Beware of this guy: Alan "midnight magic". Local con-man. I ran in to him walking around downtown. He wanted me to loan him 40 dollars in return for a life changing experience. His act was worth a couple dollars from me. A search on-line shows that he has been doing this act for quite a few years.
I live in San Diego:
For sight seeing I agree with what has been recommended. The zoo is next to Balboa park and both are excellent places to visit. Balboa park has many great museums including the Sports museum (though I have never been inside). Both are located close to downtown. You can buy Passports to Balboa park that lets you in to multiple museums at reduced prices.
The Gas-Lamp district downtown has many great restaurants and I recommend looking at yelp for what you like. Petco park is a few blocks away and there are tours available at certain times (
http://sandiego.padres.mlb.com/sd/ba...park_tours.jsp). The USS MIDWAY aircraft museum is also within walking distance.
Other popular sites: Coronado Island,
Point Loma (we enjoy going to
Point Loma seafoods), Wild animal park (though this is a bit of a drive for you). In La Jolla there is the Children's pool which is currently home to seals and sea-lions and a great walk along the coast. There are many shops in La Jolla and on Sunday mornings there is a great farmers market. Depending on the time of year and your interest in driving, the town of Julian and Anza-Borrego Desert state park are great places to visit. Both can fit into a a day trip; though, if you only have a few days I would recommend staying closer to downtown.
If you have any questions about particulars let me know.
Enjoy your trip.
Radley
(financial disclosure* I have no financial interest invested in any of these places

).