Just got back from San Diego and wanted to thank you Troy for your suggestions. We made it to Alchemy and Sambuca and thoroughly enjoyed both places.
For future reference of those searching we found a few places we liked:
http://www.vigiluccis.com/RestaurantOverview.aspx?rid=3 was recommended by our trainer who lives in Encinitas and said it was one of his favorite places. This place was a hoot in addition to serving very good food. Largely Italian staff with a manager serenading the room early in the evening in Italian. Reminded me of an old school Italian restaurant from a movie set. Had a great Antipasto Misto, Caprese Salad that should have had better tomatoes given our location, Gnocchi with truffled cream sauce, Raviolis, and Lasagna. Expected a kiss on both cheeks on departure, but got a vigorous hand shake. Got very busy later in the evening and a bit loud, but one of the more intriguing atmospheres for dining.
http://thebeachhouse.com/cardiff-by-the-sea-restaurant.php was undoubtedly one of the most stunning settings in which I've ever eaten a meal. If you can get on the patio, we got there early, it's a memorable scene. Very high tide the evening we were there, lots of surfers, and waves were breaking about 15-20 feet off the patio. Food was good, but the view was absolutely first rate.
http://www.dineblanca.com/serving/up/flash/ Turn your volume down before clicking the link. Blanca is a wine bar close to our hotel that we hit about 9:00 PM PST after visiting the zoo and we were beat. Extensive wine list as expected with a really unique menu.
Had a very good cheese and charcuterie board as everybody was starving when we arrived. Beet, strawberry, and lamb prosciutto for a salad selection surrounded by what my daughter most accurately described as "lamb clouds". Kind of a like a lamb flavored somewhat compressed cotton candy. Odd, but delicious. I had the Grilled Neville Ranch Berkshire Pork, a Day On The Farm which included a grilled loin, sausage, belly, and other forms, served with baby vegetables from seed to flower. That is the only thing I see on the current menu that apparently changes very frequently since we just returned a few days ago.
It was an intense week of training, but the weather was beautiful and we tried some really fun places that we'll remember for a long time.