Where to go:
1) Balboa Park (Right next to the zoo, but shouldn't be ingored. The museums are awesome, and Tuesdays are free if I remember correctly.)
2) The Boardwalk, Belmont Park. Start in Pacific Beach and walk (jog, rollerblade, bike) South to Belmont, ride the roller coaster, eat funnel cake, etc. A word to the wise, if you walk the Boardwalk near sunset on the weekend you will meet some "interesting" people. If your daughter is at a fragile age, you might want to avoid this.
3) Torrey Pines State Reserve. Beautiful hiking trails overlooking the ocean, nice visitors center too.
4) Old Town, Presidio Park, for a small slice of "old" San Diego. Some good Mexican resteraunts and bars to be found.
5) Gaslamp/Downtown SD, more interesting bars and nightlife, but leave yourself plenty of time to find parking.
6) Seaport village. A small shopping center right on the harbor. Lots of specialty and suveneir shops.
What to eat:
The only good thing San Diego has going for it food wise are all the little family owned Mexican eateries. Look for anything named Roybertos, Raybertos, Robiertos, Albertos, etc. They might look like crap form the outside, but damn the food is good. Always try the carne asada.
Where to stay:
Well, I guess it depends on how much you're willing to spend. But anything near the water, and North of downtown (airport) is usually pretty decent. Check this link out to find out about all things San Diego.
Sing On San Diego
Enjoy your stay!