Thanks so much for the replies!
I can't use the medium carrier because Southwest states that carriers must be 8.5 inches or shorter.
I've heard people say that the medium fits fine but I don't want to risk being held up at the gate. The flights are about 3 hours each- I'm going to open the top during the layover so she can stand if she wants. She can definitely change position in there if she wants, too, though I'm hoping she'll sleep. She's used to the carrier- it's the carrier we use for taking her on the subway, so she has very positive associations: it means she gets to go with! She hops right in and ducks her head so I can close it.
I also worry about the pee pad thing because Frida is not pee pad trained either, she goes outside. We tried to use them during the hurricane and she basically was like wtf is that? And had an accident on the floor instead, which of course we didn't scold her for.
One thing I'm hoping might work is that, because she is crate trained, I'm thinking of not putting her in the crate the night before (I often don't sleep before I travel) so that when I put her in the carrier she thinks it's still night time and will continue to sleep through the flights.
Thanks for the food advice! I think I'll just feed and water her as normal beforehand, then. I know she can hold it that long. And bring along some treats and her collapsible water bowl for the layover.