The tech museum is in downtown San Jose (thetech.org). It's OK. Entertaining, but not a "must do" thing IMO.
I don't actually live in SAn Francisco, I live in the burbs, so I'm probably a pretty bad travel guide for SF, but that won't stop me, no sir. You should also know that I suffer from that "Why would anyone want to come here?" thing since I've been living here all my life, but I do admit that there are interesting things to see.
I'd scratch in-n-our off the top of your list. Frankly, I don't think that in-n-out is all that special. It's decent fast food, and it's the only fast food around here you'll find where the food is actually fresh, and not frozen. But it is still fast food. There are better burger joints all over the country. And it would be a serious culinary crime to come to a place with the variety of food choices we have here and eat a mediocre hamburger. (way off topic, but if you want a seriously good burger, go to Reno and get an "Awful-Awful" from the diner in the little nugget on Virginia street).
And Ripley's... srsly? I'd avoid it. In fact, I'd avoid it and Pier 39 altogether. They aren't much different that any other tourist trap location. Parts of Fisherman's wharf are entertaining... a little. Some of the old restaurants have some great old photos and things hanging on the walls. An odd but interesting way to get a little historical flavor.
The angel island tour is a good one too. I think sometimes they do combo tour deals with Alcatraz.
I think... if you are coming, you have to do a few touristy things. Take a ride on a cable car (bring cab fare with you, the cable car will probably break down
You have to go to the golden gate bridge. Go park at Fort Point and walk across (or at least halfway across) the bridge. The views are cool, and walking it is kinda fun. Afterward (or before) you can tour fort point too.
You have to drive/walk down Lombard street.
Go get some Italian food at one of the North Beach restaurants that's been around for a hundred years.
Go to lands end and walk the trail back toward the GGB. It's a cool easy hike.
Consider going to the Exploratorium & Palace of Fine Arts.
Go stand on the NW corner of 4th & market and look down. You'll see a plaque that marks the former waterline of the bay. As you look off toward the bay, you see the skyscrapers (at least by west-coast standards) all build on landfill.
Go to Golden Gate Park. It's pretty cool.
Go visit Mission Dolores and learn a bit about the historically significant mission period in California History.
If you happen to be here when low tide is during daylight hours, head down the coast just a little and go tidepooling.
If you are a baseball fan, go see a game in Pac Bell park. It's an outstanding ballpark.
And if you want really, REALLY good views of San Francisco, go to Berkeley and drive up Grizzly Peak Road. In my highly biased opinion, there are no better views of SF to be had in the whole bay.
Anyhow, there are a bajillion cool things to do in SF without even leaving the city. No beachfront mai-tais under a coconut tree, but still, some things worth seeing and doing.
Oh... and definitely don't call it "Frisco."