I am experiencing aching muscles. and pain in my left shoulder is this a side affect from taking vitamin d2?

Probably not: There are several joints and intervertebral discs in the neck. These can wear out over time leading to pain. Degeneration of the joints or discs can cause neck pain, headaches, and shoulder pain. You can also get neck pain from a muscle strain. In some cases neck and shoulder pain could be related to your heart so be sure to see you physician.