Deficiencies in Vit D, Vit B12, folate and ferritin are common in people with thyroid issues and low levels can interfere with thyroid meds working.
The medical establishment do not place enough emphasise on the importance of nutrition in any illness but with thyroid issues it is especially important because thyroid hormones effect every cell in our bodies & rely on optimal nutrienal levels for synthesis.
I don't know why your endo was testing Thyroid stimulating immunoglobulins (TSI) used to measure the ability of IgG to bind to TSH receptor cell. It is more commonly used to diagnose & manage Graves Disease but your symptoms point to Hashimotos. TSI's can either stimulate the thyroid (Graves) or block the TSH receptor (Hashi). Hashimotos is usually diagnosed by testing TPOAb & TGAb.
Doctors often show complacency over testing thyroid antibodies because there is no additional offered treatment. It is up to ourselves to become educated and endeavour to reduce high levels through gluten free dieting and various supplements.
Your celiac disease results are negative (previous post) but a positive diagnosis would require a biopsy anyway. I assume you have gut issues and these could be down to low thyroid hormone which encourages inflammation by decreasing stomach acid & enzymes. Lack of stomach acid will encourage IBS, gut dybolsis and malabsorption of nutrients. Autoimmune thyroid antibodies also interfere with the production of bile acids by the liver. I have to supplement Betaine HP, digestive enzymes and bilary support.
If you are oestrogen dominant, this can increase thyroid binding proteins in the blood stream making your thyroid test results look normal even though there is INSUFFICIENT thyroid hormones.
Lack of progesteresterone can also increase cortisol-binding globulin which will make available (active) cortisol low. (Only active cortisol can pass through cell membranes and activate receptors inside the cells and only a saliva stress test will show this.) It will also impair adrenal output by interfering with the release of cortisol from the adrenal cortex. Cortisol is made from progesterone and will steal to keep supplies going, compromising progesterone levels further. However if cortisol is high it can block progesterone receptors, making them less responsive.
Low/high cortisol will also interfere with thyroid function decreasing TSH, lowering thyroid production, inhibiting T4-T3 conversion & increasing T4-RT3 conversion. It will also indirectly effect blood sugar levels.
With regard to your remaining nodules on left side... most are fine & will hopefully not require any further treatment.
Your issues are complicated and if I were you I would be looking for another endo referral. Through the National Health "choose & book" scheme, you can choose any endo you wish to be referred to. You could put another post up asking for members for advice on sympathetic endos in area postcode ------- or email email@example.com for a list of sympathetic endos/doctors that members have had positive experiences with. Be aware many of these are private.
Cortisol & thyroid connection
Ovarian, adrenal & thyroid axis
Although you don't have a Hashi diagnosis, the connection between the thyroid hormones & menstrual cycle is the same. This link explains it beautifully.
Disclaimer: I am not a medical professional and this information is not intended to be a substitute for medical guidance from your own doctor. Please check with your personal physician before applying any of these suggestions.