Balboa Park is located in the heart of SD, great place to walk around and plenty of things to see. The land was set aside when the city was founded.
My favorite activity to take visitors from out-of-town is tidepooling. I think it's that time of year when you can get decent low tides, check the charts. Cabrillo National Monument and La Jolla are two good spots to do some tidepooling, I recommend the former if you want to combine it with a trip to the national monument and see where Juan Cabrillo landed in Alta California in 1542.
Regarding places to eat, I think Crack Shack has some great casual bites. Hodads is a local institution with good burgers (a tad better than In N Out in my opinion). Bobboi has the best gelato I've ever had.
If you have any particular interests maybe I can offer some more suggestions. Nice city, lived here for 12 years but leaving soon due to the cost of living.