Having pain in neck, back of head, and muffled ear only on left side. My teeth are shifting right now from losing retainer. Could this be the cause?

Possibly. Best suggestion, see an Orthodontic Specialist immediately. The longer you wait the more difficult to resolve your problem.
Yes, possible. . Your neck pain, head pain, and ear issue could be caused by the TMJ on that side. When your teeth shift and change your bite, the change can cause premature and damaging contacts of your teeth while chewing or grinding during sleep. You may want to rule out TMJ and bite issues at your dentist prior to seeing a medical doctor just to be sure.
Possibly! Your bite or occlusion will change if the position of your teeth move uncontrollably. Malocclusion can do funny things to the temporo-mandibular joint and this in turn can cause headaches, ear aches, neck pain etc. Please go to your dentist to determine the appropriate treatment for your condition.