Hello mekin and everyone else,
I have this exact same problem as well - so frustrating. I believe I can shed a little light on it.
A couple of years ago I developed overtraining syndrome. I had had symptoms on and off for a few years as I came to the end of my Australian Rules football career (amateur - don't get excited) and I retired to karate. Overtraining syndrome is when you damage your symptom in a permanent/semi-permanent way, as result of your body not being able to recover from the training load.
I had a lot of treatment, it took 2 years to overcome and will never entirely go away.
Basically what happens is, in the case of high intensity athletes (martial arts football players, lifting etc) your sympathetic nervous system gets over stimulated. During my OTS, if I did even a fairly mild workout, I would likely get heart pounding and palpitations. After about 2 to 3 hours after finishing the workout, my heart rate would go from slightly elevated to over 100 bpm, whilst sitting quietly on a sofa watching TV. I would also feel incredibly wired, like I had just drunk 10 cups of coffee or something. Needless to say, sleeping in such a condition was nearly impossible. I would also wake up bathed in sweat.
Your SNS (Sympathetic Nervous system) is part of your ANS (autonomic nervous system) and is involved in getting you alert, ready to fight or flee, it suppresses your immune system increases your heart rate and sweat production, and gets your organs ready for doing stuff. Your PNS (para-symathetic) is involved in calming you down, repairing organs and muscles etc.
In my case, what happened was, I was trained too many times beyond my bodies ability cope, triggering a 'survival mode' response. You have 3 basic modes of metabolism - your everyday metabolism, metabolic processes when you exercise or are active, and extreme processes when your under very great stress, such as in an injury, a fight, or you push beyond what your body THINKS it can cope with. Your body is an adaptive mechanism, so it remembers how it responded to survive the last encounter. So if I trained in a way that made it think it was being pushed it would reach for the extreme response inappropriately soon. That meant my training was becoming counter-productive. Because I wasn't seeing the results, I assumed I was either soft physically or mentally - either way, train harder.
The most effective treatment I had for this was GET - graded exercise therapy. It took a lot of patience. You had to exercise very regularly but not to any great intensity. If you over stimulate your SNS, it won't come back down and for me it could trigger days of fatigue, nausea, irritability, brain fog, and of course insomnia.
I just want to stop and remark how difficult emotionally I have found all this. It's extremely confronting, and I bitterly bitterly resent it. It has made me lose confidence in my body and constantly worry about whether I am over doing things. It has also coincided with osteoarthritis (feet, hands and knees). I travel to Kilimanjaro in 1 week doing the longest trail. I am almost as fit as I've ever been but I worried about my body letting me down. Again.
Someone asked regarding blood sugar level: during my OTS I started getting post-prandial hypoglycemia. It's actually not true hypoglycemia, but your brain thinks you are hypo because it is unable to regulate insulin properly (OTS really fries your endocrine system). So I WAS testing my blood sugar levels. Yes my blood sugar level got low, and it woke me up with intense and unnatural hunger, but it wasn't low enough to be graded as true hypoglycemia.
The solution is to really cut back on carbs and eliminate sugar altogether. Eat as much healthy fat and protein as you can at a meal. Anything that can broken down easily to glucose spikes your blood sugar, causing your brain to inaccurately produce too much insulin. This mismatch causes catecholomines to be released (part of your SNS axis) one of which is epinephrine - adrenaline. And we know what that does to us physiologically. In fact, if your spike your BS and your belly is still full, your brain can misinterpret the signals as (quite often) depression. You then dwell on what might be making you depressed and then - hey presto! - you're depressed.
My guess is, if you are having these symptoms without having to go through full overtraining, or developing chronic fatigue, then your SNS is over-stimulated as result of the combination factors that can cause it to be aroused - stress, exercise, diet, inflammation. Biochemically much the same thing happens in all of these, and they are cumulative.
I hope that gives you some idea of what might be going on with you. I don't profess to be an expert, or have definitive answers - I am still struggling with the EXACT same things you guys are still. I know what I can do to manage it - it's just deeply frustrating and I resent it. If anyone is interested, I kept records of my blood sugar levels and of my HR during the worst of the OTS which I would be happy to make available.