Inner shoulder issues are caused by dis-alignment of the Humerus and shoulder line (acromial line) and dis-alignment of the shoulders acromial line with the field driveline (the imaginary line running between second base and home plate through the mound) making them a mechanical issue.
When he gets his medical release to continue, work on staying in alignment with the field driveline when he pendulum swings his arm back so his Humerus stays straight back. This is best done by having him supinate his ball arm on the way back so he arrives back with his thumb up and his hand at driveline height (top of head high). He must also arrive with his shoulders in alignment with the field driveline also. When he begins his acceleration phase he must immediately raise his elbow up and drive his humerus forwards still in alignment with the shoulders. This keeps the head of the Humerus centered in the glenoid cavity eliminating many injurious effects like ligament stretching causing a loose shoulder capsule that has the head of the Humerus travel around like a mortar and pestle that causes labrum problems. You need to make sure he throw over the top and rotates his body to recover it at finish.
Outer shoulder issues (LL shoulder) are caused by levering the Humerus across the chest (contracting pectoralis major) at recovery and can be fixed by having him pronate his pitches and rotating 180 degrees after throwing from over the top and having his elbow pop up during drive and recovery