I am sorry you are having these problems with your pet. I recently had a chinchilla euthanized after being diagnosed with malocclusion.
Your chinchilla may be having complications from malocclusion. When this occurs teeth usually have to be trimmed every couple of months to prevent tooth spurs that grow into the jaw and cause sores. Also, depending on the type of malocclusion, the roots can grow under the bad teeth and protrude into the skull and sinus cavities causing some of the symptoms you describe. Usually these will show up on an x-ray. These symptoms may return as soon as you discontinue medications if that is the case.