Younglefty - I have a 2015 that went through a similar situation when he was younger. When we moved to the states (from the Caribbean) he was 11 and his travel team started using him a lot as he was the fastest thrower. After a couple of months he started feeling pain on his shoulder. LL shoulder was diagnosed and I shut him down (no pitching) for about 6 months. It was a hard decision back them to make as I was feeling the pressure from the coaches but his future was more important than the best tournament on the world. Your son is still young and the best thing is to quit pitching for some time and see how does he reacts regardless of what the doctor says. Keep in mind also that just the act of throwing is a violent act, so don't thing that because he is not pitching he can throw a lot. I have seen a lot of HS parents saying: "if I would have known better I would stop my son pitching when he was younger". Those as the parents of the HS pitchers that had TJ surgeries and missed their senior/Jr years.
Another thing based on past experience - you mentioned above it took 3 months for the doc to diagnose a stress reaction. That to me sounds too long. When my son was having issues I went to 4 different specialists. The 1st sports ortho sent me to do an MRI with no clear diagnosis and he was like keep throwing and let me see him in 4 weeks. I got tired of the same so I kept looking until I found one that in one appointment told that the diagnosis is LL shoulder, these are the exercises for rehab, my PT will show you how to do it and you don't have to return. This is the only ortho I would trust out of the 4. But it took a lot of waste time to find the one that you know is no bull.
If the ortho starts like let me see your kid on 4 weeks to see how it goes, that to me raise a red flag.
Best of luck and remember this is the time to take care of his arm, you will have no control later.