I note that you wake up without the problem. Could your problem come from forcing your breathing? That would strain the muscles and cause the discomfort. Try not forcing your breathing and see what happens.
I had the same thing on and off , but last 2 years more so. I am 30 years old. Last two months( starting October) I had this shortness of breath everyday just like you described it , and out of the sudden it went away. I went to every doctor possible and no one gave me an answer, so I don't know what causes it and if it is truly due to stress, but I tried another thing and I don't know if it is a coincidence or what but it helped me. .. I usually work from home and sit by the computer all day long, and even though I exercise (inside) I rarely go for a long walk outside . So I started going for an hour long walk everyday, that seemed to help . Also, I took Xanax for a month at night before going to bed 0.5 mg. However, I have another problem now, I don't know if it is related or not , but I get vertigo, and vibrating, buzzing feeling inside in the left side of my body. I am going to see a neurologist soon. I wish some doctor could answer what are the symptoms that I am having. Otherwise, I am pretty healthy, not overweight, do not smoke , drink ocasionally.