@Nikki7 - Wow - sorry you're going through all that. I'm sure you know now that acid reflux is very often a sign of low stomach acid, instead of too much and doctors way too often do the wrong thing.
Anyways, the feeling full and swollen and difficulty digesting meat sounds how I felt when my gallbladder was inflamed. I was extremely fortunate in that I had a good chiropractor who did muscle testing and found this problem. He gave me AF Betafood by Standard Process - I'd suggest you read about this. It's excellent for the gallbladder and I believe it saved mine. Eventually I learned I had to start taking betaine HCL with each meal, particularly meals high in protein. Meat is one of the most difficult things to digest and requires a lot of stomach acid. I don't know how much betaine HCL you were taking, but it's quite possible that it wasn't enough. And you might want to avoid meat for awhile, or don't eat much of it until your digestive system is working better.
My chiro helped me with several digestive issues, without drugs and surgery, and I cannot recommend this highly enough. My digestion right now is 95% better than 12 years ago. My chiropractor also helped me with a liver detox.
Re your nerve damage - you likely have a B12 (and other B vitamin) deficiencies from the nexium (it sounds like you're aware of this). I wouldn't assume you have permanent nerve damage, but I highly recommend finding a competent practitioner who does muscle testing and who should be able to help get your digestive system working better and once your absorption improves, then any supplements you take will work better. I would not trust it to a doctor unless I was in severe pain etc. with a potentially life-threatening situation.