How to do this cross-reference?
I suspect this would largely be done by first determining which copybooks define files and which are for other uses.
Then take the copybooks that define files and enter the dataset names defined by each copybook. If this does not already exist to some degree, it will need to be entered.
I don't know about your organization, but the organizations I've supported had people who knew which copybooks went with which files. If this institutional knowledge does not exist, the gathering will take longer.