I am not sure if this helps, but I too sometimes wake up with a stuffed nostril. Usually the left side, but it can be either. I do not have any allergies at all and I am not on any medication. The only relief I seem to get from this Is raising the head of my adjustable bed so that I am practically sitting straight up (and it takes forever). I always thought it was because of pressure in the head-CSF build-up pushing the brain down into the brainstem or CCSVI. I also have vascular issues, but no confirmed diagnoses in this regard. An electrophysiologists thinks I passed out during the testing because of vascular issues related to EDS – not because of dysautonomia. He is also sending me to someone in regards to MCAD. I think you can rule out the allergies being the cause. I would say hydrocephalus, CCSVI, MCAD and vascular issues all being possibilities. I am sure Dr. Diana would know…