Eastside,
My son had some UCL issues this past winter. I know it can be a very frustrating time for parents and player. We went to a sports medicine center for the initial diagnosis, and they recommended a very well respected orthopedic surgeon for his treatment, which ended up not including surgery. His PT lasted for 6 weeks with no throwing at all. He had a follow up visit with the surgeon, at which time he was cleared to begin throwing. His throwing program was similar to what you had described, 20 throws at 50% from about 40 ft. on flat ground. Distance and velocity was gradually increased until he was making 80 throws from 120 ft. That was followed by another visit to the dr. to be cleared to start throwing from the mound, 40 pitches (fastballs only) at about 75%, broken into two groups of 20 with a short break between to simulate innings. The whole process took about 5 months.
Do you know at what distance your son his throwing? Maybe a longer distance could be contributing to the irritation. Also, could he possibly be having mechanical issues?
Good luck to you and your son. I hope everything works out for him.