Hard question. Do you usually have pouchitis? If so, then what do you take and does it work for you? If you do not usually have it then I wouldn't worry too much..Besides, your non pouchy co-soldiers will have the runs just as often if not more so when over seas eating foreign foods and k rations...(mind you, k rations could work well with a j pouch...they have a lot of salt in them, are generally saucy and thickened and have a good protien concentration....hmmm, not a bad idea!)
I would take peptobysmol chewable tablets, chewable probiotics to keep that good flora up high, eat tons of yoghurt, very little white sugars and avoid the sodas. Don't forget to be drinking bottled water and keep the salt tablettes that the army gives out on you at all times, they are great for dehydration!
Other than that, unless you really have a hard time with your pouch, you should be just fine.
Sharon