Glad the shoulder pain is getting better. My son broke his finger earlier this season, we saw a sports ortho and he designed a cast so he could continue to throw. He said 2-3 weeks with NO throwing could cause a lot of shoulder pain/problems when you get back. Slow gradual stretching is a must.
As for the elbow, have you ever heard of cold laser therapy? Took my son for therapy in the beginning of his JV season, he had similar elbow pain as you describe. He had three treatments, it was not costly and pitched a great JV season! 1.51 era! See if anyone in your area does it. It may be worth checking into. Good Luck