You've got me homesick! I lived in San Diego for 18 years and kept my boats at SilverGate Yacht Club for 11 years.I'm dreamin' of Coconut shrimp at Fiddler's Green, and Rubio's fish tacos, and concerts at Humphry's and the creamy white salsa at Miguel's.
I don't know how long you're planning on staying in San Diego, but I'm fairly sure SilverGate still has a 90 day "seatrial" membership deal ($60) that gives you the run of the place and includes a visitor's dock for at least a week.
The Coronado anchorage is beautiful, another nice quiet anchorage is "La Playa" next door to the San Diego Yacht Club in the Shelter Island Yacht basin, it's close to most of the boatyards, chandlerys, fuel dock and a West Marine.
Don't forget to check out Kobey's Swapmeet at the Sports Arena on the weekend...it's a local institution that gets more visitors each year than Sea World (admission is $1).
I've heard from friends in the area, that Old Town is now a shadow of way it was 5 years ago and they no longer recommend it to visitors. The State changed the park's concessions from a local contractor that ran the sales and restaurants successfully for 35 years, over to a conglomerate out of Wisconsin and has pretty well ruined it. What was a festive 19th century Californio atmosphere, was changed to a more "accurate" but dull 18th century Spanish conquest/early colonial concept. That change required that much of the lush greenery and flowers to be removed, and replaced with scub and sand. What was hugely profitable in the past now it looses money and the locals stay away in droves....ahh progress. BUT, the good news is the original lady that held the contract has a "re-creation" of the Casa de Pico/Bazar del Mundo area of the park nearby (I'm told it's doing well) as are the shops and eateries just outside the park proper.