Really? My card, which is linked to a credit card, works on both BART and MUNI.
One thing that may or may not be an issue for you depending on whether or not you’re used to it. SF has a significant homeless problem and some (but not most) people can get somewhat aggressive in their panhandling.
I am with Musicat on the Yosemite thing. You will spend 3-4 hours driving each way, leaving you with a couple of hours maybe to snap a few photos and then have to get back on the road. Add-in traffic concerns closer to the Bay Area and that schedule can get blown-up fairly quickly, and you will be cursing the waste of one of your valuable vacation days stuck in traffic. I say skip Yosemite and stay in SF that day - there is plenty to do right there. I think it’s not quite clear from the maps how big California is, and how long it could take to get around.
WRT Big Sur - keep in mind the town of Big Sur and the State Park are inland, in a nice valley, and not on the scenic coastline. The road (Hwy 1) between Carmel and Pt Sur is spectacular, and then again starting about 3 miles south of Big Sur park, but you will be getting further afield the more south you go (the road can be intoxicating!). I recommend going as far as Bixby Bridge (about 15 miles south of Carmel) and then setting a boundary there to turn around (or maybe Hurricane Point another mile+ past the bridge). Otherwise, you will want to keep driving all the way to Morro Bay.
You should also check the snow. We’ve had almost 200% of normal this year, and they are keeping the skip slopes open until after July 4th. Yosemite gets snow, and some of the roads might not be open. I haven’t seen anything on it, but it would be wise to check. But I agree it would be a waste of valuable time to go even without the snow. Great place, but not for this trip.
Some great stuff here, so all I’ll add is that I gear my trips around food, and my favourite restaurant was Frances in Castro.
And I thought Fisherman’s Wharf was the tackiest, dirtiest tourist trap I’ve been to in a VERY long time.
Sure it’s tacky, but I’ve never found it to be dirty. YMMV.
If you’re up at Fisherman’s Wharf for dinner, check out Scoma’s. It’s not a tourist trap; it’s a legitimately great (if a bit pricey) seafood restaurant.
And yes, homelessness is indeed a big issue here. It’s quite sad, and this isn’t the right thread to discuss its causes and impacts. But there’s no reason it should affect your vacation. Give them a buck or two if you feel like it. If not, walk on by. Nothing will happen to you.
Yes, you can do this, but each transit system runs its own balance. When the balance on one system goes below some threshold (say, $10), it will charge your card to reload the balance. So, for example, you could have a $15 balance on BART and a $25 balance on MUNI.
The two transit systems could share the balance and take their payments out of a common fund, but instead each maintains its own fund. The result is that the customer has more money tied up in the system. A rational, customer-oriented system would pool all Autoload funds.
I live in the East Bay and rarely take MUNI. I have authorized my Clipper card to autoload from my credit card for BART, but not for MUNI. The result is that I cannot use my card on MUNI. I pay cash on the rare occasions that I ride MUNI.
I don’t notice that SF has particularly more aggressive panhandling than any other major city. What is different is that in other places they sleep in shelters or out of sight, whereas in SF they set up camp on the middle of a sidewalk on a major street. And often are asleep midday.
I just went to the Clipper site, and it seems to me that if you put a lot of money on BART (getting a discount) you can’t move it to MUNI, but otherwise you can. My account does not have separate BART and MUNI components. I can’t see how I’d add money to BART versus MUNI if I wanted to.
And look, now we’ve scared off the tourists. 
Anecdotal, but I was informed by someone who had somewhat recently visited that, if you have a handicap sticker for your vehicle, a lot of the parking and other vehicular restrictions didn’t apply to you. I was in disbelief, but the guy I was talking to insisted, said things like they could even park closer to the trailhead than the shuttle buses went, etc…
I have no idea if true or not, just passing it along.
Go to the Monterey Bay Aquarium if at all possible.
Berkeley along Telegraph certainly did. Even 15 years ago. Couldn’t tell you what the state is today, but I remember being very surprised at how unwilling to take No for an answer the various panhandlers were.
Not to keep beating this horse, but from the Clipper website:
So you can choose to compartmentalize your funds, or not.
I was there in October and had one guy hound me for 2 blocks. But he was definitely the exception and not the rule. This was the Union Square area which is packed with tourists.
Berkeley isn’t SF. Telegraph is pretty much an open air tchotchke market, and People’s Park is close by but that’s another place where people camp out.
Granted I try to avoid Union Square, so there might be some more theatrical begging there.
Bottom line is that a visitor need not worry about any of this stuff, but just get a card and put money on it. Which makes life easier on BART and way easier than MUNI.
No weekly passes as far as I could tell, alas. When we were in New York we used the hell out of our weekly MetroCard.
Please post a trip report when you return home. Where did you go and what did you do?