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Hello. It is well documented that systemic diseases other than autoimmune disorders can also manifest with chronic itching (pruruitis). Haematological diseases, such as lymphoma, myelodysplastic syndrome and polycythaemia rubra vera, are well known causes. Imbalances in the endocrine or metabolic systems can result in chronic pruritus. Examples include chronic kidney disease, liver disease, hyperparathyroidism, hyper/hypothyroidism and iron deficiency anemia. Infections, such as HIV and parasitosis, can also be responsible for chronic pruritus, as can neurological disease, such as MS and brain tumours. Often overlooked are psychiatric causes for chronic itching, such as depression, schizophrenia, affective disorders and eating disorders. These should all be ruled out, if not already.
That said, if an autoimmune disorder is the culprit, it would be helpful to know which one it is. It would need to be addressed specifically by a rheumatologist. In general, autoimmune disorders tend to respond well to steroid anti-inflammatories such as prednisone. While not a great solution long term, they can be very helpful in ramping down the immune system (and the resulting itch) for a week or two at a time. This would be worth discussing with your doctor if you haven't done so already.
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