Start with a run so you'll feel less guilt about all of the great food and wine you'll consume later.
Palace of Fine Arts
The only exhibit remaining from the 1915 Panama-Pacific Exposition. Do a loop of this Beaux-Arts architecture on the back portion of your out and back run. Look for the swans in the pond.
Brenda's French Soul Food
Crawfish beignets. A beignet sampler. So much filling, heavy, yummy food that you can eat the breakfast leftovers for lunch.
Exclusive City Hall Tour
Not far from Brenda's this building is pretty spectacular. Take some time to admire the rotunda.
Neighborhood Walking Tours
Need to walk off the soul food and explore the city.
La Fina Estampa
Authentic Peruvian food with great lunch specials.
California Academy of Sciences
Living roof, aquarium, rain forest! Make sure to catch one of the penguin feedings if you love penguins as much as I do.
Japanese Tea Garden
Sure it's a bit touristy but there is something peaceful about the Japanese Tea Garden that transports you.
Americano Restaurant & Bar
Right across from the Ferry building. Enjoy the outdoors, a wine and the swanky setting before heading off to Alcatraz.
Night tour of Alcatraz. Depending on the time of year you can see great sunsets with panoramic views of the Bay or eery fog fit for a prison where Capone lived. The only thing which better is a swim from the island to San Francisco (with boat support of course!)
Since every tour of Alcatraz ends here.Eat some Hog Island oysters if they're still open.
Under The Bay Bridge
Watch the Bay Bridge light show from the ferry building.
One of the best places for quality lamb in San Francisco. Plenty of amazing other dishes as well.
I would stay at: cavallo point
Since it's my perfect day I'd splurge and stay in the Marin Headlands. Gorgeous views of San Francisco. Good food and plenty of hiking/running/biking trails right outside your door. Dress for chilly evenings/mornings.