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Cortisol reaction from exercise?

1.5 years ago, when I just turned 28, I started to feel this "full" feeling in my stomach and a burning feeling in my throat in the morning. It's very uncomfortable and sometimes gives me a headache by the afternoon. I went to the doctor who advised me to track what I ate and when I felt the symptoms. Since then I have tried everything- experimenting by cutting out certain foods, coffee, drinking less water, more water, everything. I am stumped. It has driven me crazy, since some days I have the symptoms and some days I don't. I eat very healthy- low amounts of flour, sugar, dairy, wheat. I have exercised every day for the last 6 years- a combination of cardio and strength training. I really enjoy getting my heart rate up, even if just for a short time, and sweating to feel like I've had a good workout. It is hard for me to skip working out or do something leisurely. When I decided to take a break from working out recently and just walked instead, I was symptom free. I have continued to be symptom free as I've been only walking. So my question to you all is:
What is this I am experiencing? Is it something to do with cortisol?
I have PCOS (Polycystic Ovarian Syndrome), and I experience insulin resistance, which has gotten worse over the last few years. I wonder if it has anything to do with that. I am a 29 year old female, 4'11 and 127 lbs. My BMI is 25.
Why would exercise make me feel this way?
Should I visit my doctor for more help? Tests?
I have searched and searched for others who experience this and have not found one. Has anyone else experienced this?
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