Could it be stress related or a panic attack? I sometimes can have issues breathing where I am under or over breathing and also yawning a lot. Taking a small dose of Xanax (.125mg-.25mg) takes this away and I can breath as clear as day and as deep as I normally can. Not saying this is your issue but it may be worth looking into to.
I know it's a terrible feeling. I've had to take sleep aids for months in order to even fall asleep. The best thing to do is try to steady your breathing. Keep telling yourself that you are getting plenty of oxygen even if you don't feel like you are...( most people with this problem have excellent oxygen blood saturation)...Hyperventilating makes it worse...so breathe slowly. If the feeling comes on while I am laying down, sometimes sitting up to take a breath sometimes helps me. It is exhausting though. You may want to be checked out for that silent acid reflux. I know a lot of people on here have said that Nexium is a lifesaver and does a lot for their symptoms.
My shortness of breath started when i was probably 8 and now i'm 32. I can recall crying my eyes out and my dad taking me to countless doctors to no avail. It is somewhat manageable for me now, but burdonsome. What helps me most often is this:
Try taking a deep breath in thru your nose, as deep as you can.....as you breath in with your nose, push your stomach out, then exhale thru your mouth......keep trying this, it helps me often, but sometimes takes a few minutes.....saddly, most doctors will blow you off.....i've had stress test, cardiograms, lung saturations, you name it.....all good.....but as i type this, i'm still getting frustrated cause i have a feeling that i can't catch my breath, and sometimes have to force myself to yawn just to catch it. Good luck.