My heart goes out to meet you - I've been dealing with difficult to manage endocrine problems for years, after a particularly difficult birth. After years of feeling crazy, moody and unable to sleep more than 3 or 4 hours a night, a thyroid test finally showed up a little out of the normal range. Further testing revealed my thyroid gland is not functioning at all, but has a very large tumor (benign) that is causing hyperthyroidism. It's a big deal and a big mess, and as serious as it is, it still took years to get an accurate diagnosis. Thyroid problems can be like that, and the thyroid gland affects your body's metabolism. Low thyroid function is a possible reason you cannot lose weight.
I would suggest seeing a very skilled endocrinologist, especially since you have already diagnosed endocrine issues like the estrogen dominance and adrenal fatigue. In my experience, the endocrine system is delicately balanced, and though the problem may be one issue, it will affect the endocrine system as a whole. In my case my thyroid tumor caused adrenal fatigue and hypoglycemia, but neither of these two problems were the "real" problem.
I would eliminate all stimulants and depressants from your diet for a good long time (think months to years). Including caffeine, chocolate, sugar, and alcohol. In fact simplify your diet as much as possible, eating as many whole foods as you can, and eat less than you generally do. This is not a weight loss strategy, but rather a way to help your body eliminate toxins and excesses of the endocrine system. Although, it should help with the weight loss goals, too. I've had a lot of success modulating mood swings with a period of taking in very simple food (homemade chicken broth with brown rice, plain toast, yogurt) for a day or two to cleanse my system, and drinking a good amount of herbal tea made from a variety of roots, especially licorice, wild yam, burdock and dandelion roots. These roots have the properties of balancing out hormone production and toning the endocrine system, and they have been the best thing I've found for dealing with the mood swings. You may want to consult with a good herbalist, or a Chinese doctor, for an herbal blend that suits your particular situation.
All the best to you as you sort out this difficult situation. I agree with you that prescription meds like antidepressants are not the way to go. I tried these once, and it made my problems worse, and more difficult to sort out. Birth control pills will effect your endocrine system, and might be helpful or might not. They may cloud the real issue, and make it more difficult to get an accurate diagnosis. Work with a good endocrinologist and a good herbalist - insist that they do a thyroid function test, and any other testing that seems reasonable, plan on allowing some time for this to resolve, but don't give up!!