You are really making me flashback. I usually avoid injury type discussions because the correct answer is "I am not a doctor. Go to the doctor".
But, the timing of this is exactly what happened to my son. At 13, the season was probably over in late July with the playoffs, which is when he started complaining. (didn't want to pitch because his arm hurt)
When fall ball started, he started complaining again about "the same pain", so I took him to the doctor.
"Shut it down. It takes a long time for these things to heal. It might not be ready in the spring."
The age, the timing, and long tossing words are the triggers making me respond because of the similarities.
Yes, I agree you need to throw to increase arm strength.
But, you need to make sure he is healthy first.
Some long toss with a stress fracture is not OK.
It will need complete rest to heal if that is the problem.
Now, I will be curious as to what the doctor says, so let me know.
Stress fracture sounds like an awful injury, but is very common with young ballplayerss because of those growth plates and throwing a baseball.
I think they increase about the time the boys really start to grow.