Personally, I would move La Jolla to the top of the list. It is the epitome of what Southern California is all about. Spend a day wandering around the Cove, enjoying the beauty of the coast and popping into some local boutiques, coffee shops, or gelaterias. Maybe make your way up to Torrey Pines - watching the paragliders is a site unto itself - and if you're up for the hike heading down to Black's Beach is totally worth it (just be aware that the beach is "clothing optional"). There are a number of great restaurants in La Jolla but I'll second (or third?) the recommendation of George's at the Cove. I'll admit I'm a bit biased, as my Fiancé and I had it recommend to us when we first moved here as a "special occasion" dinner, and now three years later are planning our (small) wedding there, but it is indeed a special place. World-class food, incredible service, and breathtaking views. Try the fish tacos.
We also love the zoo - and prefer the safari park to the downtown zoo - but both are outstanding.
The museums in Balboa Park are "good" but not outstanding - if we want to see world-class museums we head to LA. The Midway is pretty cool and I really enjoyed it but my fiancé really wasn't interested - so just decide who in your group would enjoy it and plan accordingly. If you're into military history you'll love it.
We live in Little Italy and LOVE the farmers market. I love seeing markets when I travel, and if you do to you won't go wrong there. It could make a great afternoon wandering around the area and grabbing lunch from a vendor.
I think seaport village and Old Town are tourist traps and absolutely NOT worth your time. I always feel bad for tourists (especially those that come off a cruise ship and only have a few hours here) who think seaport village is San Diego.
Petco is a beautiful park - only drawback is that you have to watch the Padres.
Where are you staying? That would very much determine what things are easier to do than others and how much time you'll need.
Enjoy your trip! Let me know if you have any questions.
Edit to add: Also, don't go to Tijuana. Seriously. Nothing good will come of that.