The Stinking Rose, when I went a few years ago, was a great idea that fell down on execution. It was mainly basic Italian food with a some garlic flavor. I love garlic, and the food just wasn't that garlicky. Still, some people love it.
If you'd like a more distinctly San Franciscan restaurant, you might try
Steps of Rome Trattoria in North Beach (not too far southweest of Pier 39). Wonderful Italian staff, killer friendly atmosphere, and you don't need to be a hipster like their sister restaurant Steps of Rome. Two caveats: the menu is structured like a traditional Italian, with antipasti, primi, and secondi courses, feel free to pick and choose out of order. Second, the staff tend to be gay, to a more or less flamboyant degree, extremely charming, but if it's not your thing you don't have to go. My Ohio-born mother loved it.
One of my absolute favorite restaurants is a Basque place called Piperade in the financial district, also fairly near the tourist areas. Distinctive cooking, somewhat seafood heavy, but something for everyone. A well-chosen wine list with many selections from Catalan country.
If you can make plans a few weeks in advance, try the Slanted Door in the Ferry Building (a couple miles south on the Embarcadero). Vietnamese with a French twist, it grew from a fashionable hole in the wall to one of the signature restaurants in San Francisco. Believe it or not, one of the best dishes is chicken in clay pot, but they also specialize in crab, "shaking" beef tenderloin, and spring rolls. Again, a great wine list with lots of riesling if that's your style (sorry, not much in the way of Aussie riesling). Reservations are essential.
For a drink outside, stroll down a few piers (1-2 km?) along the embarcadero to Pier 23. Cold beer, pub food, large outdoor patio. You might have to wait on the weekends for a table.
Whatever you do, check the weather before you leave. Not that I know anything about you specifically, but when the wind kicks up and brings in the sea breeze, San Francisco can require a jacket even in summer. Enjoy your visit.
Walt