I only have general advice, because I am ATPL (A) licensed, and have not flown helicopters.
Keep doing the exercises, they will eventually work. I had bad pain in my shoulder, (not caused by flying), to the extent that I could not lift my arm high enough to put a coat on any more. I also get a (different) pain in my shoulder blades after I have been on my iPad for a time.
Here in the UK, it is almost impossible to see a doctor, so I had no access to medical intervention so instead I did shoulder exercises, and my shoulder pain has now completely gone - I am now back to normal and can put a coat or a jacket on now.
The pain between my shoulder blades only happens when I have been slouching over my iPad for an hour or more. If I make sure my posture is better, that pain does not occur.
So, my suggestions are to continue the exercises, and maybe talk to a physiotherapist to make sure they are the correct exercises for you.
Secondly, in the helicopter, experiment with your seating position. Try setting the seat higher, lower. Seat tilted more backward or forward. Try the seat moved forward, then backward. I don't know if pedals are adjustable, but if they are try different pedal positions. Try changing your feet position on the pedals.
I am sure that you will eventually find some position that works for you, helped by the exercises.
Good luck, and let us know how you get on
