I was just hopping on to check for something else and saw your post, so I don't know much about you or your journey (so forgive me if I'm passing on redundant things or telling you things you are well aware of!), but I will pass on the things I've been taking that seem to have stopped that middle of the night anxious mind for me.
I do have low adrenal function (and low thyroid), and yet I began having relief from what you are describing when the following were added to my protocol by my MD (and before I added adrenal and thyroid support):
Kavinace ultra PM - neurotransmitter help. It has a precursor to GABA, and other calming and sleep-inducing things (including melatonin). I give myself a good 10 hours or so from when I take it to when I will need to be awake, if I'm needing to function any the next day, as it does make you drowsy and if you are up and in light too early, you will feel nauseous as it also has melatonin (which makes me feel nauseated if I am exposed to light when my body is drowsy on melatonin).
I also added progesterone at night - I'm postmenopausal- and I also use topical low dose testosterone and estrogen in the morning, but the added nighttime progesterone is what my MD says to keep taking for that anxious feeling (in addition to the Kavinace).
I added Neuro-mag (Life Extension) a month or so later at bedtime as I was waking again occasionally with that racing mind. It crosses the blood-brain barrier to feed the brain, but is controversial in Lyme world as magnesium is used by pathogens - Buhner says the bugs will get what they need and so we might as well take it because our bodies need it so much (magnesium). It seemed to be just the thing to keep me sleeping well.
I've also felt that has a connection to my body detoxing at night and I've occasionally done epsom salt baths before bed to get some calming magnesium into my body (and bypassing the gut where the bugs like to use it), especially if I feel my body is detoxing/herxing more than it might be able to process.
As for detoxing/processing all the toxic byproducts, I'm using Pekana remedies (Itires, Renelix, Apo-Hepat), bentonite clay and charcoal (mold toxicity) and liposomal glutathione. I'm sure several of the herbs I'm taking also contribute to detoxing and processing of toxic stuff. When I keep up with all the detox things and keep things moving well, AND take the bedtime stuff, I sleep pretty well and even fairly restorative. I do usually wake up to use the bathroom, but have been generally drifting right back to sleep afterwards.
Hope that is helpful!