For 2 years, my 7-year-old dog has been getting worse and worse. We have had test after test done on him to try and find out what the problem is, and all tests come back either normal or negative. He can't eat or drink without vomiting due to megaesophagus, so we spoonfeed him little bits of food at a time and he drinks out of a rabbit water bottle. He can't walk more than 5-10 steps at a time without stopping and sitting in a begging pose to rest. He walks on the top instead of the bottom of 1 foot.
My vet thinks it is a neurological problem, not an injury. His rear end drops when he walks, his back legs are constantly bent, and he has a bad cough. He also doesn't have very good control of his bladder.
It appears that your dog has a significant neurological problem. Unfortunately, these can be quite challenging to diagnose. Your description sounds like a neuromuscular disorder (something affecting nerves outside of the brain/spine, muscles, or the junction where nerves communicate with muscle). The most common disorder that causes megaesophagus and weakness is called myasthenia gravis, but there is a chance your veterinarian has already tested for this.
Metabolic diseases like hypothyroidism can also cause neuromuscular disease, but not typically to this degree. Inflammatory or degenerative diseases can also cause nerve/muscle disease. I would recommend having your dog seen by a specialist (a veterinary neurologist), as it sounds like you have a good vet who has been very thorough, but has still not identified the cause.
Sometimes a fresh pair of eyes can provide some insight into a case; they could start by simply reviewing any of the tests your vet has already performed. A neurologist should also be able to localize the problem within the nervous system and make sure that this is not a brain disorder. They may recommend additional tests, such as an EMG, spinal tap, or even a nerve or muscle biopsy. Without a diagnosis, treatment can be difficult and so a veterinary specialist may be able to provide direction.