Hi - from what I understand there is a couple of things that happen in the body:
Stress - even though you are no longer having stress - the body may not have let go of the fight/flight response that you have been through. This has a cascading effect in the body.
Cortisol - strips the body of magnesium - you just can't take enough to reverse the effects of cortisol - this can lead to a build up of calcium (hence arthritis and fibromyalgia - where calcium builds up in the body).
The lack of magnesium - causes the kidneys to be distressed - and therefore your body will be dehydrated. The water and minerals can't get into the places they need to be.
With the kidneys under stress the body does not move flouride or mercury. If you drink flouridated water or have amalgam fillings you may be affected. In a class that I sat with 20 people (who are all alternative health care professionals) there was only 1 person not affected by mercury. Mercury also blocks zinc, Flouride blocks molybedenum which is needed to mediate zinc and copper. Aluminium also blocks zinc.
Zinc deficiency afftects stomach PH - which affects assimilation of all minerals including zinc. Zinc makes the stomach more acid, which is what you need stomach to be. Zinc is also needed for the immune system
Also if your body is still in fight/flight - this may affect your digestion. In this state the body is not programmed to be digesting food - as it needs all resources to be in fight/flight.
What causes the body to stay in fight/flight? It could be a trauma or series of traumas that make this happen. When the body has had a trauma it can cause tension in the jaw muscles, which may create structurual and neurological imbalances, dehydration and mineral deficiency.
Kinergetics is a type of kinesiology that works with this pattern in the body - it works on the TMJ (jaw muscles) and in many cases this can give great relief to people. Also hydration pathways in the body are corrected too. If this does not give relief, then trauma and other corrections may be needed.
Hope this is of some help to you.