Start your first morning in Puerto Rico with a local staple for breakfast at an island institution. Head to La Bombonera, on San Francisco Street, and try out a delicious mallorca. After, I'd suggest a walking tour to ensure you get the most out of your day in the old city. You can check out my suggested tour, or download a walking tour onto your ipod. Another option is to take a tour. I heartily recommend Legends of Puerto Rico, which conducts both a day tour and a fantastic Night Tales in Old San Juan tour.
As for lunch and dinner, here are a few suggestions. For lunch, enjoy a hearty 'Rican meal at El Jibarito on Sol Street. If you crave something a little more sophisticated, head to El Picoteo in Hotel El Convento for excellent Spanish tapas.
If you follow my tour, you'll end the afternoon at the magnificent Raíces Fountain. From here, it's a short walk to Fortaleza Street, where you can try one of the restaurants on the list for Day One, or, for a truly transporting meal, head to Panza, one of Puerto Rico's most romantic, elegant, and outstanding restaurants.
Day One and Two covered the old city; on Day Three, you'll see the rest of Puerto Rico's capital.