You can try Monsieur Benjamin, a newer restaurant near Absinthe (very good, but make reservations well in advance, especially during Opera season) with gourmet dishes and appear very open to a diner's specific requests. Do try their house special ice cream. Trust me, it'll be the best ice cream dessert you and your nephew will ever have!
Gamine French Bistrot is very good. Service is always excellent, friendly, and cozy enough restaurant where you can easily relay special requests to the chef. Believe it or not, their escargot is the best I've ever had, even better than the ones I've tried in Paris!
For fancy Italian, Acquerello may be a choice for "gourmet." It's along the lines of La Folie/Fleur De Lys, but a bit more open to "menu" alteration, though with limitations. I'm not sure, but I suspect they may be more open to being flexible, where the aforementioned ones surely will not be receptive to any alteration.
Traditional Italian, do try North Beach Restaurant on Columbus. Authentic and better than the fancier ones, in my view.
For Pizza, try Tony's in Northbeach. Long lines and popular on Yelp (one of the few they've gotten right, but avoid House of Nanking at all costs). Try the deep dish Sicillian pizza with their special sauce on the bottom of the plate to soak in the dough.
For Chinese cuisine, try Koi Palace and stay with their seafood dishes. Their other stuff is overpriced and overrated, but their seafood is world class and prepared in the finest Cantonese style. For Yum Cha, try HK Lounge on Geary (avoid Chinatown) and/or Dragon Beaux (further down on Geary - newer, more expensive, but better).
Finally, try Molinari's sandwiches. Many like the Southbeach (fancy sandwich), but I prefer the traditional Northbeach.
Have a great time!