I'm definitely not as experienced as others on this board, but hopefully I can help. For starters, you seem like a really caring teacher to work with. I have a feeling most of your students really like you!
Here's are my ideas, and I really hope some other teachers here can offer some suggestions. I personally learn a lot from threads like this.
Measures 1-4: I would have him play those much slower. Those were about twice as fast as measures 9-12. Perhaps he should practice measure 1-12 very slow with exaggerated dynamics, so he can feel the piece at one tempo. I would also perform with him at the same time during the lessons, and use the metronome.
I have found that when you do "exaggerated practice," such as playing very slow, exaggerating the dynamics, the hand movements, etc., it tends to drive the point home.
This is not mentioned a lot, but I believe there also comes a point for some where students lose interest in the piece, and do not have the capacity to practice in a focused manner. I've had this happen with students, and I usually move on, and supplement, to ensure they develop the proper skills and techniques.