But first thing's first - Jon/Ellen (that is, Ellen in Jon's body) needed to get back into his own body. Who knew what that boy was doing with it? He had seen his original body (occupied by Jon) leaving with his transvestite boyfriend, so by now they were probably both at his boyfriend's apartment.
Grasping the stone, Jon/Ellen said "I wish I was back in my body again ... but also had the wishing stone with me," he quickly added at the end. He didn't want to lose the opportunity of using the stone. But nothing happened. The stone didn't grow warm or flash or anything. Maybe the wish couldn't be granted for some reason?
Okay, then if he couldn't get his own body back, then maybe he could change the one he's in to be more to his liking.
"I wish I was a girl," Jon/Ellen said.