The clothing-optional section is at eastern end of the beach, starting right around the sand ladder. If you'd prefer to steer clear, there are alternate trails up to the bluffs.
If available that day, buy a loaf of their levain bread to take home.
Definitely try to go during a Giants game. A unique experience indeed.
Incredible place. Really good "shelf talkers" (those notes on the shelves pointing out good selections). Don't forget they have two storefronts, the main store plus the annex down the block. Fiction, travel, music and mags are in the latter space.