Jon couldn't change himself. But he could change Katie. And the wish was for him to look like Katie. So that was the way to change back... just transform Katie first. Either the wish would make him look like the new Katie right then and there, or else he could change it so it would.
His first wish, then, came shortly. "I wish that for the next day, Katie is physically like I was just before she transformed me."
Jon didn't see any change in himself (herself?)--but a shadow lifted from his eyes. Not a metaphorical shadow, a real one. Because the bunk bed's top had just vanished--it was a regular bed now! Which meant it worked. For the next day, Katie would no longer be Katie. He was the only Katie, and the room was a one person room.
"Now, I wish that the Katie that I'm physically like is the Katie of right now, even if she's very different before or later." That way after she changes back, he'd stay himself.
The stone worked, Jon had to glance to the side... and it suddenly got dim. There was enough light from outside to see with, but the lamp in the room had vanished. In fact, almost everything had vanished. Katie wasn't Katie for the next day, and Jon wasn't Katie either, so the room belonged to nobody. It was bare. He got up and walked around... and immediately realized that something was weighing down his chest. It was his bra, filled by his breasts. The breasts! He forgot about those. He couldn't undo that!
Jon sighed, and dashed out of the room. He couldn't reverse the transport wish, so he'd have to undo it manually, by getting out of the house, before he could get home for real. He ran past Katie's surprised sister (now an only child for the next day) and made for the door. He opened it and ran out onto the open air. "I wish I was at home in my room!"
He was standing in his room. Which didn't look normal, because the same thing had happened which happened to Katie's before. There was a bunk bed, for one thing. Some things there were too many of, and some were too big. Katie, of course, or whoever she was now, would be like Jon for the next day. Why did he say a day? He should have said ten minutes or something. This was a bad idea... everything wouldn't really be back to anywhere close to normal until the next day had passed.
The door opened. Jon saw someone who looked just like himself--without the breasts--and could only say "Katie?"
"Yeah, it's me."
"You're... uh...."
"Jon, what's the matter? It's me. Your brother. Keith Thomas Madison, K.T." replied the boy.