I experience shortness of breath from fatigue on days I do more than I should. But if you are back to your usual exercise schedule that probably doesn't apply to your situation

I also used to get short of breath from my chest muscles being locked up due to anxiety. the things that helped were yoga - it opened up and relaxed my chest muscles and also acupuncture. Therapeutic massage might help too so you can be more comfortable while you figure out whether its anxiety or neck issues