For a 11-13 mile run (not sure of the total distance), I would head through the Presidio to Baker Beach, then follow the water back up to GG Bridge, continue following the water back to Fisherman's Wharf, then head back downtown along Columbus.
Run up Kearney to California, turn left on California, right on Taylor, left on Broadway. Broadway will end at the Presidio - just continue heading in the same direction (west). Eventually you'll have to cross Park Presidio, then turn right onto 15th. From there pick up the dirt trails to the left of the abandoned hospital. Those go all the way down to Baker Beach. From there you just follow the trails along the water back under the bridge, along the Marina Promenade, through Fort Mason, along Beach Street. I'd try to pick up Columbus in Fisherman's Wharf so you can see North Beach. That'll take you to the base of the Transamerica Building, which is downtown and close to your hotel.
You'll see everything on this run - Nob Hill, Grace Cathedral, crazy steep hills, Pacific Heights, amazing views of the Bay, the Presidio, the Pacific Ocean, the beach, Golden Gate Bridge, the Marina, North Beach, Transamerica Pyramid.