What Causes Pain In The Neck While Having Herniated Disc Disease?

I have some ongoing issues with my spine, cervical, thoracic and lumbar. Approximately 2 years ago, it was found that I had a severely herniated disc in my neck that caused spinal cord damage in my neck at C5/C6. I had fusion done and I have had ongoing pain since then. Fast forward to today, I am still receiving care for pain in my neck and beyond. I saw a physical therapist today and he feels that my smaller muscles in my neck and trunk are not firing at all. All the main muscles are being over worked and they are trying to make up for the increase of work. Is this related to my spine problems perhaps? Also, in my neck, there is a section in the front to the right side that is completely numb since the surgery. I don t know how deep the numbness runs but could it be affecting the small muscles in my neck on either side of the thyroid and cartilage there.