Your symptoms are suggestive of immune mediated disease like; systemic lupus erythematosus, Raynaud's disease, dermatomyositis, scleroderma, rheumatoid are the possibilites. So if you have not consulted a rheumatologist; that would be the first step. I am sure that your adrenal function tests and thyroid function tests must have been done. Still consulting an endocrinologist would be prudent (if not yet done) as hormonal dysfunctions are the other diagnostic possibilites for your symptoms. Following work up would be suggested (some may have been done for you);
1) Complete blood count,
2) Erythrocyte sedimentation rate,
3) Thyroid function tests,
4) Muscle enzymes;
5) Anti-nuclear antibodies (ANA)
6) Adrenal function test
9) Anti-SSA (Ro) or Anti-SSB (La)
10) Coombs test
11) CT scan of abdomen
The immune mediated diseases and hormonal disorders are the prime causes of generalized manifestations affecting all the body systems, especially when the infective causes are ruled out.
Please feel free for your follow up questions.
I would be happy to assist you further, if you need any more information.