Our vet took a look at him and was amazed. Somehow the swelling has made his genitals disappear! They aren't there at all, to the point that you can't tell if Boy is a boy or a girl. He (we will continure to refer to Boy as a male until proven otherwise) now has a special prescription salve to put on his bottom three times a day to help bring the swelling down, prevent infection, and hopefully speed up the healing process. In the meantime, he will have to stay on his "special diet" for the rest of his life.
We're not sure if Boy will ever look normal in the back end. He uses the litter box and pees and poops like any other kitten, but the logistics of how are fuzzy at best. Like I said, he has no genitals at the moment, only one swollen bum. It doesn't slow him down though. He gets more upset that he has to stop playing for a minute when I apply the cream. Boy will not be able to leave until his bottom is healed up. I'm still looking for a home for him, but he won't be able to go just yet.
The orange kittens also went to the vet for goopy eyes. They are on a prescription for eye drops twice a day to clear it up and prevent it from spreading. Incidents like this make me happy that the two litters are kept separate! The eye drops make their mouths foam up (instant panic, but a call to the vet cleared that up and the kittens are fine about an hour after the drops). They should be on track to be healthy for their neuter surgeries - provided they weigh enough. This does not look promising right now as they're pretty small. Now that they are starting to eat mom's food, I'm going to increase the food I'm giving them. Perhaps an all-you-can-eat buffet of quality food will bulk them up. I can hope.