This sounds like classic CFS. The shifted body clock is a give away IMO. Awake into the night and then sleeping late.
It's an autoimmune illness which is why you feel so terrible. Your right about your digestion and your stomach acid. Also probably correct about adrenal fatigue even though I dislike the term. Your adrenal glands are most likely sub functional but not enough for a synacthen test to show anything abnormal.
The pain you feel on your right hand side is most likely not your liver, although it will by working extremely hard due to increased intestinal permeability syndrome, it is your stomach and/or transverse colon that is causing that discomfort. I sometimes get a very similar thing.
Your pituitary gland could be hypo functional if your Chronic-Fatigue-Syndrome is very severe and as a result, so will your thyroid function. In which case your whole hormonal system will be functioning abnormally.
Frequent urination? Due to low blood pressure and resulting in dehydration.
Short term treatment:
Get some magnesium ASAP. Magnesium Malate is good and not too expensive. Source naturals tablets are what I use. You would benefit from x2 the dose but start slowly and work up. This is such an important mineral and your cannot make use of it due to your digestion. Mag Malate is quite well absorbed, there are even better but much more expensive.
Methylcobalamin. Fine a cheap source if you can because you need a hell of a lot of it. Loading your blood will help a lot. I take 25mg/day. Work up because it could kickstart methylation. Starting with a low dose maybe 1mg capsules/tablets might be a good idea. This should reset your body clock and you should sleep.........at much more normal times. It will also stimulate the activity of your TH1 suppressor T Cells which should lower the IgE antibodies which are produced by your immune system reacting to the large food molecules being absorbed into your bloodstream through your hyper permeable digestive system.
There is an eating style which might help. It helped me enormously, for me it was the difference between walking miles and having virtually no symptoms and struggling to even get out of bed.