DW and I will attend DLR for the first time this Summer!

We also are looking into a possible 4-day getaway in San Francisco this coming September. We are from the east coast and have never been to San Francisco before. We are interested in the "first timer" typical tourist things to do in SF, as well as the Walt Disney Family Museum, of course.
We are pretty laid back but conservative. We are looking for a somewhat romantic experience as well.
The two things I need help with are:
1. Where, o where to stay? Hotels are fine. We can't pay Disney prices on this one. I'll say our budget is between $150-$275/night for lodging.
and
2. The Walt Disney Family Museum. Please point me in the right direction if there's info here on the DIS about it. If not, then I'm gonna need some expert advice from those who've gone before!
As always, thank you so much!
My favorite city!
We live outside the city and tend to visit several times a month, depending on our other plans (there is so very much to do in the Bay Area in general!).
As to where to stay, I can't recommend specific hotels as we never stay anywhere there. But for tourists, I would recommend either the Union Square area (my personal preference) or Fisherman's Wharf (definitely very touristy, although we often spend lots of time in that area due to having two young children who like Pier 39).
Big question- car or public transit? Car gives you more freedom, but parking can be stressful and expensive. If you are doing public transit, then I would map out what you want to see and plan your days by checking into the transit schedules and options.
There are of course all the typical tourist activities, such as Alcatraz and Fisherman's Wharf, and the Golden Gate Bridge.
We haven't been to the WD Museum yet as I am waiting for our youngest (DD2) to be older. Since we live here, there's no real rush for us. But I have heard many, many good things about it, so I am sure you will find more than enough to keep you busy for the day. The Museum itself is located in one of our very favorite areas of the city, The Presidio. I highly, HIGHLY recommend taking some time to explore The Presidio. Crissy Field and Fort Point, in particular, have some spectacular views of the Golden Gate Bridge and city. We love picknicking at Crissy Field and flying kites, but that will be challenging for you as a tourist. Still, definitely worth a wander down through.
Off the Grid is located right across from the Museum and is open Sundays 11-4 if you visit on a Sunday. Otherwise, you might check out their schedule as they are all over the area and might be a good option for you to check out one of your other days. If you are Star Wars fans, Lucas Arts is also in the Presidio, and you can get a picture with the Yoda statue.
Another area we really like is Lands End. You can grab lunch at the historic Cliff House, check out the ruins of the Sutro Baths, then walk along the cliffs at Land's End. It's amazing that this place is within the boundaries of a large US city. There's a visitor center to check out there as well. It's breathtaking views. There is a memorial to the USS San Francisco along the way, too, made out of the damaged bridge wings of the ship. She was one of the most decorated ships of WWII and fought in the battle of Guadalcanal. Then there are the West Fort Miley Batteries. It's all very cool, historically, and a beautiful and peaceful walk.
Also down on that side, close to the Presidio, is the gorgeous Palace of Fine Arts (designed for the 1915 Panama-Pacific International Exposition). If you like taking pretty pictures, this is a great spot. It's a highly photographed spot, but I don't think as many tourists go since there isn't much to do, per se. If you do one of the double decker bus tours, I believe they stop here.
Golden Gate Park is another great place to visit with many options for things to do. The most popular being the California Academy of Sciences (really need a morning for this, but it's a great place), Conservatory of Flowers, Japanese Tea Garden (one of my favorites), and the deYoung Museum (if you aren't going to the museum, you can still pop in and take the elevator up to the observation tower for a free pretty view of the city). There are also many free things such as walking through the botanical gardens, visiting the Buffalos, seeing the Windmill, stopping by Koret children's park to slide down the concrete slides (sooo fun!).... there's endless things to do here. The park is right near the Haight neighborhood, so you can also walk around that area and grab dinner, or head down to the Beach Chalet for drinks and an ocean view (right out over Sunset Beach).
If you are up early because of time zone changes, then Twin Peaks is a lovely place to try to catch the sunrise. You have the best chance here of anywhere in the city. Otherwise, it's a nice, quick stop for the view.
One of our favorite touristy things to do with visitors is take them on the boat ride out to the Golden Gate Bridge. You can purchase tickets right at Pier 39. It's through the Blue and Gold Fleet. The talk they give on the ride is really an wonderful overview of the city's rich history.
Down along the Embacadero, our favorite place to eat is the
Ferry Building. SO much good, local food! We snack our way through, but we always get some empanadas from the little stand near one of the entrances. If you visit Alcatraz, I highly recommend walking up here for lunch because it is far better than the options right near where they have you board.
Walking tours of the city are my favorite. So much of San Francisco's beauty is in the details of the neighborhoods, such as the steep streets with stairways built into the sidewalks or the gardens you can peek into. I would browse through
San Francisco Walking Tours to find a free (!) tour that appeals to you, and if you don't want to do it as a group, then map it out to do on your own. San Francisco is really a walking city.
I could share so much more, but I'm sure others will have some great tips as well. Have fun!!! September is one of our most beautiful months, but I cannot stress enough that visitors should bring warm clothes and plan to dress in layers. It can be downright cold during our foggy mornings and then change to quite hot by our sunny afternoons and then get cold again when the fog rolls back in for the evening. Also, temperatures change across the city, so while it may be warm and pleasant by the Ferry Building, it will be cool and foggy by Sunset Beach.