Overtraining? Did I do this to myself?

Please forgive me for yet again raising the subject of fatigue. A fortnight ago I was diagnosed with hypothyroidism, which is believed to be the source of my unresolved tiredness, trouble losing anymore weight, and mental fog. My TSH was 3.44 which, quite controversially, does or does not fall within acceptable hormone ranges (either below 5, or below the newer limit of 3). My free T3 was not tested, but my free T4 was normal. My family has no history of thyroid problems.

My physician said there was nothing abnormal about these seemingly incongruent results. I have no reason to distrust her, but my skepticism has increased after reading several online articles that link symptoms of hypothyroidism with overtraining. I started consistently exercising in May 2012, stopped for two months to travel, resumed exercise, and then stopped again in March 2013 for another two months of travel. When I returned home in May I had no worrisome fatigue.

When I resumed exercising I greatly increased the amount of strength training, having previously been very much a cardio bunny. After a month I noticed that my weight wasn't shifting very much. Though I had made strength gains, my muscles were always sore–not DOMS sore, but clearly never fully repairing. And then fatigue as I had never before experienced began, and continues to plague me.

Is it simply coincidence that my thyroid began to perform poorly around this time, or did I do this to myself? I visit the gym five times a week (strength training 2-3 days for 50 minutes, 120-140 minutes of cardio a week), allow for two rest days, and am otherwise sedentary. My calories vary (as you can see in my diary, if you choose), but I always eat above BMR; I have a problem limiting my calories, not meeting them. I ask this because I would prefer not to take medication for the rest of my life if, as some people found, their thyroid function returned to normal merely after taking a break from exercise.

Once again, thank you for indulging my persistent inquiries with your patience. Whether limiting my exercise or having to depend on medication, I hope I can resume weight loss, abolish this ridiculous fatigue, and not feel like I shuffled out of the Walking Dead.