Here's something I saved once from Dr. Lowe's site you might find helpful:
Question: Thank you for the best and the most informative website. I am 59-years-old and been hypothyroid since 1998. After reading your website, I switched from T4 alone to 90 mg of Thyrolar, which has both T4 and T3. After being sick all those years on T4, I now feel good. I exercise three times a week, and I’m on my feet all day running around taking care of responsibilities. But despite feeling well, my basal body temperature is always low. This morning, for example, it was 96.5EF under my tongue, and 95.5EF under my arm. Although I feel well now, I wonder why my temperature is still so low? What does it mean? Have you had other patients with low body temp?
Dr. Lowe: You may know that Dr. Broda Barnes championed the use of the basal body temperature. He advocated using it to identify people who are hypothyroid, and to adjust their dosages of thyroid hormone. I think it’s prudent to keep in mind Dr. Barnes’ tempered view of the basal body temperature. He believed that it is the best gauge of improvement available to hypothyroid patients, but he noted that the test isn't perfect. Based on my clinical experience, I agree. But then, no test is perfect.
At this time, we're conducting two studies in which we're measuring patients' resting metabolic rates and comparing them with their basal body temperatures. We’ve tested many patients, but so far, we don’t see a statistical correlation between the two measures. The important question is, why not? We suspect that the lack of correlation has resulted from the patients using different quality thermometers—some that give accurate temperature readings, others that don’t.
Unfortunately, patients cannot get glass mercury thermometers anymore. We have some of these, however, and we’ve compared temperature readings with them to readings by digital thermometers. We’ve found that digital thermometers often give readings that are almost a full degree higher or lower than readings given by the glass thermometers. So, the lack of correlation may be a result of poor reliability of digital thermometers. Obviously, before we can finish the studies in a meaningful way, we must work out this problem; otherwise, we could reach a false conclusion about the usefulness of the basal body temperature. Of course, we won’t allow that to happen.
Over the years, we've found that some patients’ low basal temperatures don't increase, or don't increase much, despite them fully recovering from their hypothyroid symptoms by using T3 or Armour Thyroid. Molecular and physiological principles lead me to a conjecture about the persisting low temperatures of these patients. We all have enzyme systems that maintain core body temperature by causing cellular energy to escape as heat. Thyroid hormone regulates the production of these heat-regulating enzymes. The enzymes decrease in hypothyroidism, leaving most patients colder. When the patients undergo effective thyroid hormone therapy, the enzymes increase and, in turn, so does the patients’ body heat.
But the patient whose basal temperature doesn’t increase with effective thyroid hormone therapy is presumably different at the genetic level. The genes that code for the temperature-regulating enzymes in the patient are less responsive to thyroid hormone. As a result, her basal temperature remains low, as yours is, despite her recovering from all other indications of hypothyroidism.
Whatever the reason for persisting low temperatures in any individual, we know such patients exist. For them, the basal body temperature is not a useful gauge of improvement from a particular dose of thyroid hormone. Because of this, we prefer to measure the resting metabolic rate, based on the patient's oxygen consumption at rest. This test is more reliable when done properly. But, of course, it isn't as accessible to patients as basal body temperature test.
http://www.drlowe.com/QandA/askdrlowe/
Linda
Low Basal Temperature and Thyroid 
