Wow it has been awhile but it looks like we finally got answers. I'm posting this in hopes it helps someone else one day. Since the last time I posted we had an MRI. The MRI showed a chiari 1.5 malformation. Neurologist refered us to neurosurgeon who recommended surgery. We had brain surgery on Monday and are now recovering. Still to soon to know if this fixed our issues but the neurosurgeon is very confident that it will. Her brain stem tonsils were hanging down into the spinal cord region causing increases cranial pressure and pinching the nerves in that area. Surgery was able to remove a peice of the top vertebrae and some of the skull to create extra space for the brain.
After seeing many doctors who ruled our condition as acid reflux we finally saw the right doctor's to get us the answers we needed. Hopefully this comes in handy for someone some day. Will post a follow up in about a month on the results of surgery.