Yes you can have low fat cheese on this plan. One cheese that I recommend people try, if they are brave is soy/tofu or even almond cheeses. These all are low fat and most importantly, have low saturated fat if any. They do taste a little different than regular cow's milk cheese, but I hapen to like them. I've found them at my local grocery store, whole foods and trader joe's of course.
Don't count on nuts to get your fiber requirement. You'd have to eat a LOT of nuts for it to really make much of a dent. I too have IBS as well as have had two surgeries in that area and I make sure I get a minimum of 35 g of fiber a day, per my gastroenteroloigst's recommendation. I usually get close to 50. Quinoa, bulgar wheat, whole wheat tortillas, popcorn, veggies are all ways I get my fiber.
One thing to keep in mind with whole wheat this and whole grains that, even if you get whole grain chips, pretzels, crackers.. etc... they still are chips, pretzels, and crackers. Use very sparingly and not as an every day treat. This plan emphasis real foods and no matter how you dress them up, those things are still not as good for you as other things.