You should definitely have a hidascan done, as gall bladders cause a lot of the symptoms you describe. IBS can cause the same symptoms too, so that's why you have to have it checked to rule it out.
Unfortunately, while you are deployed, you are going to be subjected to the worst kinds of food imagineable, so I don't think you're going to be able to avoid things that mess you up very much. But you may want to talk to someone and tell them that you suspect you might have a food allergy, and do they have special meals for people with gluten allergies? If you could at least try that, it might answer the question of gluten allergy for you.
If it's your gall bladder that's bad, or if you have regular IBS, the gluten-free diet won't hurt it any. Some things to avoid with bad gall bladders, though, are fatty and greasy foods (no pizza, no fried chicken) and caffeine. If they start handing out No-Doze pills, pass; those mess up a regular person's stomach to some degree; someone who has a sensitive gut will be even worse. Fatty and greasy foods, caffeine and alcohol are bad for IBS people as well, so no matter what your problem really is, you won't hurt yourself by getting off those things. Besides, during the first Gulf War, more servicemen were killed in drunk-driving accidents than died in combat, so you can at least do your mates (as well as your guts) a favor by staying sober. If you can get yogurt, that's a good way to get both probiotics and calcium daily. If you can take some Caltrate 600 w/ vitamin D with you, try taking one pill up to three times a day to see if that doesn't help with the D and some of the cramping; it's worked wonders for others.
And I would stay away from apples and apple juice. No one product is known to make people with gut problems of all kinds worse than apples and apple juice. You say that they bother you intermitently anyways, so you might as well avoid them all together. Some people, though, do have some luck with cooked apples, including applesauce, so if you really love them, you might try them that way.
When you go back to civilian life, get yourself a job with health insurance; please, for pity's sake, don't rely on the VA to take care of your medical needs. The most depressing place I have ever been in my life was a VA hospital when my great-uncle was dying. I've been in nursing homes before that were brighter, cleaner, and cheerier. And as the US VA and the British VA are taking a pounding for their lack of care right now, it's not a good time to rely on them; definitely go private.
Just remember that over there, everyone's an enemy unless they prove otherwise. Stay safe, watch out for Iranians (those people are crazy and they're not afraid to jump the border and take hostages), and God bless.