I have trouble breathing sometimes when I'm lying down...I also had horrid acid reflux while on high-dose prednisone...I had a chronic sore throat from the acid coming into my mouth every night...Gross!

Do you have big bumps on the back of your tongue? I mean, towards your throat? If you do (and I have these) this is from the acid irritating your taste buds...The small lymph tissue at the sides of my tongue is also irritated from the acid...

The acid itself might be causing you to feel like you can't breathe well...It can also cause wheezing...