I hope you feel better. I also took Protonix (for 2 years). It can't hurt to get a second opinion from a doctor. I went to my doctor and her advice didn't help, unfortunately. I don't think she knows much about what it's like to be on these PPIs. She wanted me to try and get off them, but it was my own research that gave me ideas on how to do it. I'm watching my carbs, I eat slowly (chewing well is so important) and I've taken papaya enzymes if needed and a probiotic twice a day. I also am not eating 3 hours before bedtime and I've elevated the foot of my bed. Oh, the biggest thing I think I've done is give up sodas. I think those screwed up my stomach, but I still kept drinking my one Coke per day. The fizziness is so addictive.
I wish you luck, Heather!