Perseus, sounds like you are having a pretty rough time of it, hence the open call to the forum.
I am putting forward unqualified opinion. I have been an airline pilot for 40 years.
As QDM says, back to the doc, but I suspect that you have beaten a well trodden path down that route for some time. I am assuming that you have faced up to all the more serious possibilities and had them checked out, you can't be doing with the burden of that kind of worry while flying.
Question. Are you sure that your stomach is contained below the diaphragm? You say that the hernia is small, but there should be a clear determination that there are no adhesions that leave the top of the stomach tacked at the wrong latitude.
Perhaps, and only perhaps, the tiredness should be divorced from the rest of the symptoms, inasmuch it would be logical to feel washed out while all the other factors are nagging at you.
The other possibility that comes to mind is, I have to confess, one of my hobby-horse beliefs. When a problem persists and causes long term distress, there seems to be a very counter-productive tendency for the body to auto-clamp various muscles, be they sphincter, blood vessel, or other. The cyclic wind-up can be circadian or random, and unbelievably painful, or not, perhaps simply causing other symptoms to mask what is going on. Relaxation techniques are usually not enough, the loop has to be broken with prescribed and if possible, specific muscle relaxants. Strangely, once you catch your sub processing at it, the need for drugs often seems to all but vanish.
Do keep the thread going.
LR