At Ghirardelli Sq, try the ice cream. If the line is huge, there are 3 or 4 places (all Ghirardelli), so just look around to see if there's one with a shorter line.

I would also add Alamo Square for the famous view of the painted ladies with the Financial District in the background.

And for the best shot of the GGB (like the one in the first picture in your post) head up Hawk Hill on the Marin side.

Also worth checking out the Point Bonita lighthouse at the end of that road. Though make sure to check the opening hours.

Muir Woods National Monument is also great if you haven't walked among redwoods. Can be crowded in the main area, but there are also longer trails that are much more secluded.

Enjoy your trip!