Thanks for the great info. Very helpful. As for the orthopedist, he is a local ortho specializing in sports injuries and considered to be a solid doctor. Due to a lack of testing (range-of-motion diagnostics/listening), we have opted for a second opinion. I felt that more extensive testing might have revealed more information. I also think the possibility of surgery warrants it.
He agreed with your comments about an MRI. He said it was tough to call on an MRI without contrast. I'll definitely push for that on the second opinion. He was very hesitant to suggest surgery on a patient this young (13) and preferred the PT at this time. He explained that he put little faith in an MRI and wasn't fully convinced that it was a partial-tear at his age and given his history.
As for the off-season, my son didn't play. He spent it lifting and in lessons (hitting/pitching) only. That is one of my largest reasons for concern. I want to eliminate the cause of the problem but cant pin-point it at the moment. I'm not sure that it wasn't the weight-lifting rather than the pitching. He's always had fairly good mechanics BUT has thrown his fair share of innings (has always been pitch counted though).
At any rate, we are discontinuing throwing for the holidays and will start PT early next week. After the holidays, we will see the Tallahassee Orthopedic Clinic, who I was told handles Florida State Univ's injuries. Hopefully the second opinion will reveal more or simply confirm what we already know at this point.
Again, thanks for the comments. Have a great holiday!