My first suggestion is probably going to sound pretty lame, but hear me out. I’ve got at least two dozen trips to SF under my belt (2 trade shows a year for eight years, for a week at a time, plus another eight or ten trips for other business-related stuff, including a couple of two-week stays in 2004 and 2005). I’m no big fan of overly touristy stuff. But when I took my wife and youngest daughter (then 18 months) out for the July 4th weekend a couple of years ago, we spent one full day on one of the package bus tours – in our case, the SF City Tour in the morning and Muir Woods/Sausalito in the afternoon. My rationale was that I wanted my wife, who’d never been to SF before, to see some of the sights outside of walking distance from our hotel on Market (Golden Gate Park, Twin Peaks, Mission Dolores, The Palace of Fine Arts, the Presidio, Fort Point, the Golden Gate Bridge, etc.) without the hassles of public transport with a toddler, and without the hassle and expense of renting a car in SF (parking is difficult to find most places and expensive once you do). I also wanted to make it out to Muir Woods, which I’d never done in all the times I’d been in the area (had been up Mt. Tamalpais on the back of a motorcycle and as far up as Stinson Beach, but never actually to Muir Woods).
I think if you’ve got Friday morning on your own, you might consider doing one of the half-day city tours to see some of the sights outside the Nob Hill/Union Square/Embarcadero/Fisherman’s Wharf/North Beach/Chinatown/Market Street areas (all of which are within walking distance or a cable car ride or two from your hotel). You’ll also be able to get familiar with those areas so that you’ll be able to make some decisions about what you want to return to on your own or with your girlfriend. Or you could do one of the hop-on/hop-off shuttle tours so that you could set your own pace, but a lot of them don’t hit the more far-flung sites.
The California Street cable car line will take you straight from your hotel down to the Ferry Building, from which you can catch the vintage streetcars for either Fisherman’s Wharf or Market Street. You can walk from the hotel to Union Square and Chinatown, and from Market Street and Powell you can take the Powell-Hyde cable car line across town to Fisherman’s Wharf, or vice versa. Lots of good places to eat in the Union Square/Market Street area, but things change fast enough that I’m loathe to make any specific recommendations – trust the locals on that front.
OK – a couple of restaurant suggestions. I usually stay in the Union Square area, most often at the Prescott or the Andrews, so I know the restaurants right around Post and Taylor pretty well. Ar Roi, a solid, unpretentious Thai place on Post at Taylor, has been a favorite for years. The food has been consistently good for long enough (back to the mid-nineties) that it’s not likely to have tanked recently. It’s not a terribly romantic atmosphere, but if you want a really good Thai meal at a very reasonable price (as I recall, most entrees aren’t much over $10), this is the place, and it’s practically the closest of the Theater District/Union Square restaurants to your hotel.
If you want a cozy, romantic Italian dinner, you can do worse than Fino , also on Post near Taylor (almost catercorner from Ar Roi), in the street level of the equally cozy Andrews Hotel. The menu’s not particularly adventurous, but it’s pretty broad, and I’ve never had a meal there that was at least very good – often it’s extremely good. It’s not hip or trendy, but very nice and has also been consistent through the decade and a half I’ve been going there.
Shalimar, on Jones between O’Farrell and Ellis, is the most authentic Pakistani food you’ll find, according to several Pakistanis and Indians I’ve worked with in SF. It’s in the Tenderloin (but only by a block or so, and is close enough to major tourist hotels that it’s relatively safe) and is not the place to go for atmosphere (you order at the counter, and the decor is strictly utilitarian) but would be great for a reasonably priced excellent lunch, assuming South Asian food appeals to you.
For breakfast, I really like going to Lefty O’Doul’s. I’ve never tried it at other times of the day, but you can do a lot worse, and the ambiance is fascinating – it’s a slice of SF from 50 years ago. Ditto Sears Fine Foods, though it’s now owned and operated by the same company that owns the ubiquitous (three of them within a few blocks of Union Square) Lori’s Diners.
Generally speaking, you should be safe enough in the areas you’re likely to be in – you will get panhandled, but generally not threateningly. One point, however, is that you should resist any temptation to cut across to Market Street from your hotel between Van Ness and Taylor, or at least Jones, if your tolerance for aggressive panhandlers, junkies, hookers, and general weirdness is at all low. The Tenderloin area is gentrifying, and the influx of Vietnamese families has helped somewhat, but it can be a bit nervous-making even in the daytime if you’re not prepared for/used to it. North of Pine, and east of Taylor, and you’ll be fine.
In addition to the other good suggestions so far, I recommend the San Francisco Maritime National Historical Park, where you can go aboard the three-masted square-rigged Balclutha, and see other historic ships up close and personal.
There won’t be any baseball games that time of year (opening day won’t be until around the first of April), but you can do a tour of AT&T Park (formerly PacBell Park and SBC Park), which is an amazing park – among my favorites.
I’m gonna buck the trend and say you might give Alcatraz a miss. Tickets are expensive and impossible to get if you wait too long (a month in advance is sometimes not enough, though this time of year a week is probably about right) and will will burn up a lot of time on one thing – time you could be spending seeing more of the city. You’ve really only got two full days, and you’ll burn almost 1/4 of that on Alcatraz if you do it. Do a one-hour bay cruise instead and you’ll get to see Alcatraz pretty close up, as well as Fort Mason, Fort Point, the Golden Gate, Sausalito, Angel Island, the Bay Bridge, etc.
Speaking of burning up time, I’ve spent far longer on this than I intended already. Hope this helps.