I lived in SF for 10 years and although the golf landscape has changed quite a bit since I left in 1996 (such as the closing of San Geronimo in Marin County a few years back -- that broke my heart)...there is one under the radar 9 holer that was quite the treat back then.
It's called Gleneagles and it's down in McLaren Park in the central south part of the city.
I always loved that place. VERY difficult. Very natural terrain built on the side of a mountain/hill, and minimalist design. Was originally designed by Jack Fleming who worked with MacKenzie and Hunter on Cypress Point and has the 9 holer inside of Harding Park named after him. It also has a very cool small clubhouse/bar/proshop, and a single guy that bought the place and saved it from going under, who is the starter, bartender, greenskeeper, etc. holds court there serving drinks, food, and sending people off the diabolical first tee.
I always thought it was a cool place for purists. Give it a look. You could certainly do the Presidio course and 9 at Gleneagles in one day. Playing Gleneagles during twilight and the sun going down is quite serene.
A fun fact that blows me away is that when I lived there, Harding Park was kind of dumpy, but had relatively decent bones and only about 6600 yards or so. Sometime after I moved the TPC group acquired it, gave it a massive overhaul and lengthened it significantly. If you play that, think about the fact that it was once sort of an ugly duckling compared to what it is now. And also beware, I have had multiple friends who have played there and had their cars broken in to while out on the course. Unfortunately, that is all too common all over SF these days from what I'm told. You'd never think it'd happen at a golf course though.
I can't suggest Gleneagles highly enough. Give it a look.
I quit golf for 11 years. I started back playing my last 2 years in SF when I was driving a Veteran's Cab and some other drivers found out I played college golf and got me back into it. They took me here.
I miss that place immensely. I wish I had discovered it sooner. I will most certainly go back there another time from Atlanta at some point in my life.
http://www.gleneaglesgolfsf.com/Safe travels and have a great trip. If you do play the little Gleneagles gem, let me know what you think of it. Jim