Has your lifestyle become more sedentary as of late? Exercise does a lot of great work for your body. It could also be a matter of nutrition or a blood disorder.
Have you tried an experiment of eating just nutritious food and exercising an hour a day?
You're in the most likely place in the country for Lyme Disease. Do you remember a tick bite or a red rash or a flu like illness before these symptoms started? Usually Lyme in New England involves sore joints and muscles, but not always. I wouldn't have thought of it for you except for the shoulder spasms.
My Lyme includes lots of GI issues, incl. stomach pain, malabsorption, bloating, loose and/or bulky stools, viitamin B12 and magnesium deficiencies, as well as fatigue, headaches, shortness of breath, cognitive issues, rib/chest wall pain, gallbladder pain, sleeping problems, and a few others I won't bore you with.
http://www.ilads.org/lyme_disease/B_guidelines_12_17_08.pdf
Check out the symptom list in this document. If you think Lyme is a possibility, find an LLMD (Lyme Literate Medical Doctor) who is familiar with the disease and knows how to make a clinical diagnosis. Most doctors don't recognize the non-joint symptoms of Lyme and believe the blood tests are perfect, which they're not. Up to half of people with Lyme test negative on antibody tests. You can also check out the Lyme Disease forum for more stories and feedback.