Cortisol is released in different amounts over the course of the day. If it's too little or too much at one time, it can still be too much or too little at another. Get a diurnal salivary cortisol test. Diurnal means "daily" or "over the course of a day". You order a kit to take samples of your spit at four points during your day and submit it to a lab for analysis.
Take your samples at waking, 5 and half hours after waking, 11 hours after waking, and 16 hours after waking (if you're on a 16-hour wake cycle). For lots of people this means roughly 8 AM, noon, evening (4 PM) and 11 PM. But it really depends on your own sleep/wake cycle.
Try to have your sleep schedule as regular as possible, and stop taking any hormonal supplements a couple weeks before.
Search this forum for "salivary cortisol results" for examples and discussion.
Should you stop the thyroid meds? I don't know. You say you experience some bad side effects. I think that's a good sign you should stop.
I believe the Depression and brain fog can be fixed by other means, if you have "Adrenal Fatigue". Consider lysine for the depression. And licorice for the cortisol imbalance (but stop taking it before testing cortisol levels).
For testing supplements and drugs, "start low and go slow". I also advise "try it three times": I think folks don't realize that we get a lot of variation in our health levels — the presentation of our illness is chaotic and hard to follow. If we take a supplement and feel great, it may not be the supplement, it could just be coincidence. Then we get attached to doing something that's added time, effort, and money when it does us no good, or, more frighteningly, we have a bad experience coinciding with something that would have helped us and lose out on benefit. Not that any of us need to be more anxious about anything while we're having AF...
Read up on AF. Try Dr. James Wilson's book as a primer. And spend time at Dr. Lam's website. And read this forum from page 1. Sounds like you haven't been ill for long and that your illness is brought on by a more acute situation rather than a long-term tendency towards anxiety and stress, so it may not take you long to recover.
Oh, and make sure to reduce your stress and anxiety. It's a steep uphill battle otherwise.