Anne Marie,
I went through a similiar experience when I went gluten free. I had a surge of improvement about two weeks into it and then backslid for about a month. After about 2 months gluten-free, the surge of improvement came back. I am now running about 1 min per mile faster on long runs and almost 1 min 15 sec. mile faster on short runs. If I get glutened, my times automatically increase for about a week.
As far as diet, I try to avoid simple carbs unless I need a quick pick me up (before a soccer game for example). I stick with fruits, vegetables, protiens and nuts. It is an adjustment from the endurance mantra "carb load, carb load, carb load" but I am doing so much better.
I have also learned that sometimes I just have a bad run and it is not the Celiac's fault because non-celiac runners also have bad work-outs too. Yesterday is a good example. I live in North TX and it has been unseasonably cool and wet so far this summer. Yesterday was one of the first really warm days and very very humid. My long run was very very slow, but not from anything related to Celiac. It was the heat.
Don't give up. One of the things that gets me to the gym to lift or out to run is to tell myself my bones need the resistance training. It's good for me. It motivates me because I don't want to miss soccer games or runs due to stress fractures. Silly I know, but it is what get me there
Kat.