504 for the individual is not really the vehicle for a complaint against the entire state for multiple individuals. However, a critical mass of individual 504 complaints sharing a root issue would stand a good chance of gaining notice that a systemic problem is in place. Whether or not the OCR's case processing would encourage them to turn the matter over to the Department of Justice is a big unknown.
OCR has the ability to open district wide compliance reviews. Obviously, this would not be a prompt, individualized investigation to resolve a single complaint which should be a factor for consideration. It is also one that is not in the control of a parent filing a complaint.
There is also an established reporting structure for civil rights issues into a larger database.
http://ocrdata.ed.gov/. I have no personal experience with it but I do know of ed civil law professionals that do make use of it. With enough data it could show a probable cause for investigation. That is a wild guess on my part but not a completely uneducated one.