They are most likely from your thyroid issue. Thyroid (under or over active) will also cause fatigue, swollen lymph nodes in the throat. I have B12 deficiency, it has not caused my lymph nodes to swell in the past, and I have researched it lately and have not found anything to state that it does. But I also found out during my research and from my recent Dr that B12 deficiency is an autoimmune disease. If you have one of these, you can have multiples. So its a good chance you have a few of these going on. The thyroid issue is another one.
Are you taking B12 injections?