Yeah hopefully they will get better. Have you thought about holding off the exercise until your eating is better? I know that may sound crazy but when I used to go to the gym I used it as an excuse to eat- I've worked out I can eat these choc bars. I know that's not what you are doing but maybe if you stopped running your appetite would curb, you would be able to eat less- therefore shrink the stomach and then exercise may not make you feel hungry.
It's just an idea. It's tricky finding what's right for you, I started exercise on Friday. I'm still in pain from it now haha x