First of all, if you are on a candida program that is suitable for your body , you should be feeling better in 2 months and not worse. If things are working,you should feel better in a matter of weeks, just the reverse of what is going on. So if there is no improvement, then something is wrong. That is an alert to you already.
Secondly, hair loss is usually tied in to androgen imbalance and this frequently seen in adrenal weakness. The fact that your thyroid is worse also is consistent with the overall picture that your candida program is weakening your adrenals. I will not go into every detail aspect, but if you read my paper called Adrenal Fatigue related health conditions on my website http://www.DrLam.com,
it is clearly explained there.
Most candida program fails because the body's constitution is not properly taken into consideration ahead of time. The best program to rid candida will backfire if your body cannot handle it. You may not feel it, but your worsening symptoms is often your body's cry to alert you.
Candida problems are seldom standalone. Its almost universally present in those with adrenal fatigue. So it is already given. Am I concern? Of course I am. But I look at the big picture. Many have candida and adrenal weakness and is stable. The moment they try to rid the Candida, they actually get worse. If your body is strong enough defense wise, you don't need to worry about candida. The key is how to keep it under control. And the best way to do candida type programs such as detox etc etc is to do it when the body is ready, and only when the body is ready.
Most people do not factor in the down side to candida programs, and that is why invariably most fails. The more advance the adrenal issues, the higher the failure rate,and for good logical reasons. You cannot push the body to do things when it is not ready.
The fact that you are not better is a red flag. Don't fight your body with your logic, as you will end up loosing again and again. Your body never lies to you and is always, repeat always, right. Everything the body does is for a good reason. So your thyroid is worse now, and your hair is coming out. To me , these are warning signs your current path is not welcomed by your body.
The key is to have a plan that prioritizes what is important and how to deal with it systematically. Most adrenal fatigue patients, like you, have a body with many moving parts that are dysfunctional. I urge you to return to your doc and seek another approach. Timing is critical. The right thing done at the wrong time is wrong , and that is where clinical experience comes in and the difference between a pro and an amateur. This is where the bookwork stops and experience takes over. What you are experience makes perfect sense to me and not confusing at all. Its easy to solve.
If you are not feeling better, and you don't have a good reason why , and you don't change, you will continue not to feel better. That is basic logic. So do spend some time with your doc and ask why if the candida program is so good, you feel lousy ? Alternatively, find someone who really know what they are doing to help you and you will be well ahead.
I am not trying to debate with you whether Candida is at the root of the problem or not. I know Candida is there, and so are many other bacteria, virus, parasite that we have yet to discover. As a clinician, my job is to get you better. That is the bottom line. One way or another, your clinician should recognize failure and change course if things are not working. If you are not feeling better, no matter what your theory is, you are on the loosing end.