I have had intermittent pain in my neck, chest and arm for over a year. I had a thermagram that showed inflammation. What could be causing the pain?

Many things. Wide spread inflammation is usually associated with autoimmune disorders. The circumstances you described, fibromyalgia is a likely diagnosis. A year is too long to wait while having pain. See a doctor.
Cardiac. It is important to rule out cardiac pain. See your primary care physician for evaluation.