Large studies (involving hundreds of people with MSA) have not found a common cause of MSA; environmental toxin (including well water) may be a precursor, but it begs the question why are not spouses, who have been exposed to the same, suffering from MSA, too? So far, no link to stress, though that has been suggested.
Research: Probably, what you said about research spending could be said of all rare diseases. I’ve heard, but I forget, the proportion of people with Parkinson’s to people with MSA. I know it’s huge. Usually research dollars are awarded based on the number of people with the disorder, not the severity of the disorder. There are exceptions, of course, but your point is correct — the millions spent on MSA research is nothing compared on the hundreds of millions spent on Parkinson’s, Alzheimer’s and other neurological research. Some day a cause/cure for MSA will be found; my hunch is it will be when cures for other neurological disorders are discovered.