You didn't mention what -- if any -- budget constraints you might have. If money is no object, the Francis Drake is elegant and centrally located. But San Fran is studded with hotels in a gamut of price ranges. Last time there, wife and I stayed at the Best Western Civic Center on 9th St., just a couple of blocks from the Civic Center and the Museum of Asian Art. Very reasonable room rate, free parking, microwave and 'frige in the room.
Dinner recommendation: on the one evening you want to splurge, go to Harris' Restaurant, 2100 Van Ness Ave. Pricey but the best steak I've had in my entire life, and I've lived a fairly long life. It's apparently a well-kept secret because we dropped in on the spur of the moment, no reservations, and didn't even have to wait in line.