Thank you for writing.
A symptom of hypothyroidism is actually feeling cold, rather than an internal heat. So we cannot say if this internal heat you are feeling is connected to your thyroid condition. It may be but it's not a usual symptom. However, "internal heat" is certainly something that can be caused by thyroid disorders.
Menopause could still be the culprit - your hormone replacement therapy may not have helped - did you try different dosages or just one?
In some people, diabetes could be the cause or GERD (acid reflux).
I think it's a good idea to keep trying to regulate your thyroid numbers. It can take many tries. Talk to your doctor about this internal heat to see what she/he can do about it.
Please keep us posted.