You have quite a complicated health picture and to get to the bottom of your conditions, I would suggest looking for a local medical herbalist who can take your case and medical history in full.
However, the most common reason for hypothyroidism is 'autoimmune' thyroid disease and you are more likely to have relations who have had an underactive thyroid or other autoimmune disorders such as Vitiligo, Pernicious anaemia, Addisons disease, type 1 diabetes, coeliac disease, rheumatoid arthritis or Sjogren's syndrome.
If so, then your joint pain may also be inherited and I would suggest you try a 6-8 week course of Atrosan tablets, as these are licensed for joint pain but won't interact with any medicines you are prescribed.
For faster relief from joint pain, you may wish to apply Atrogel morning, noon and night, though it is the Atrosan that will produce the longer lasting effects.
Aches and pains are also one of the symptoms of ME and this is another complex condition but in my experience and when diagnosing ME, there is often a major emotional or physical trauma that preceded the onset of symptoms.
Working through this with a CBT practitioner while self-helping your shattered adrenals with remedies such as Siberian ginseng, eating every 3 hours, avoiding stimulants and improving sleep quality are the key measures to overcoming the condition and those associated aches and pains.