Have you talked to a doctor about it? I guess I'm used to mountains (and I fly a lot) so it's never been a factor but 5,000' seems low to feel it in such a drastic way.

I know when I fly on long trips, especially if I am sleeping, I can wake up and feel out of breath. I also get really puffy...but that's fairly common and I am not moving around.

I'm sorry I can't be of help but I'd say to go get it checked out. Hopefully there's something you can do, I'd hate for you to feel miserable