I've also had iron deficiency on and off, but not severe. I think the two issues are unrelated and are coincidental. The good news is that a vitamin supplement prescribed by your primary care physician should do the trick.
Regarding the leg cramps, these are one of the main symptoms that led to me knowing something was wrong prior to my diagnosis a couple years ago. As the other poster mentioned, after the correct dosage of medication was determined, (which took a few months), the achiness went away. Recently, severe achiness in my legs returned, I went in for bloodwork, and sure enough my thyroid was off again and meds need to be adjusted.
I also have Hashimoto's Thyroiditis and as the thyroid sputters out, sometimes flare ups and their aftermath will lead to dosage changes. Good Luck! What a good hubby for doing research for her!