If you are still having hot flashes on the Premarin then I would really recommend looking into bioidentical hormones. I understand your worries about cancer risk but it cannot be good for your body to go without female hormones 20 years longer than it normally would, either.
B12 deficiency can have some serious and even irreversible consequences, so if yours was low, I would follow that up. Get a test for anti=parietal cell antibodies (an autoimmune inability to absorb B12) and a repeat B12 level (which could also just be low due to poor absorption in the small intestines). Get another copy of your thyroid tests and post them.