Dear Bluebird,
...I see a dark stranger in your future...
Just kidding. :-)
That's good you are doing the active exercise before your shoulder exercises. Try keeping the same breathing and focus going while you do your shoulder exercises. Like focusing on breathing into the lower dan tien, and aligning your posture, tongue up, etc... If you do this , the exercises won't mess with that good feeling you generated in your active exercise. You can improve on what the doctor gave you as exercise, by adding the internal part.
Also, there is nothing wrong with focusing on your shoulder during level I exercises. You don't have to dwell on it, but you can initiate and/or stimulate healing there if you direct some attention there as you exercise. Most of your focus can be on the given visualizations, but you certainly can be aware of helping that area, within the context of each exercise's attributes.
love,
gallen