DId you ever get a solution to your problem. That sounded very distressful to me, and as a patient who offers from Crohn's disease with a lot of similar symptoms, I was just worried that you still weren't properly diagnosed as that can sometimes take the doctors quite some time to arrive at a conclusive diagnosis. The symptoms you describe could be the symptoms of a Crohn's disease patient. Not, that I am suggesting this is what is wrong with you, but it is certainly something that needs checking before it gets too severe. Crohn's is very painful and untreated it only gets worse. On the other hand it is a manageable disease under the right circumstances, which include regular checkups, the right medication, and a diet that suits your individual needs.
On second thought, I believe you might benefit from a GI apt. not affiliated with military. You might have "emptying problem" wherein timing is off in stomach to duodenum transfer. Hence, increase digestive enzymes being "dumped" in bloodstream. You will be okay, just report any weight loss and request albumin/ other nutrient levels/ calcium etc....with NEW doctor!
Most likely Celiac. You've had an immune response to what you were exposed to in Iraq/ or stress while on duty.
Eliminate ALL wheat/gluten!
Son,
Frequent yellow and black diarrhea is in no way normal. Scans won't always show stuff wrong in your guts, and could be it's just not blocked yet. A bowel that does what yours did, can do it again, and at the very least you've got bleeding going on and an infection, neither of which can be ignored. I don't want you to suffer anymore, either. You need a complete workup at the VA, or county health department, or an internal medicine doc of your choice very soon.
GG