The gas problem is pretty common and is a general issue when you have candida. I believe it is unrelated to die-off or the diet; it just happens more when you have candida.
I still get a lot of gas after eating protein personally (6 months into diet) and am long over the die-off stages. I still get a bunch of gas after the coconut bread and almond butter with rice cakes (stage 2 item).
My naturopath feels that it is only related to protein and certain food items; he prescribed me a vitamin/supplement called zypan which completely eliminates any gas. I typically get a little gas before taking the zypan and within 30 minutes of taking it, the gas is gone for good! I take 3 zypan with lunch and highly recommend this supplement if you are interested in getting it; standard process makes it!