First, if people are winging it, your first problem is going to be standardization and sterilization of the data. If everyone is using excel, for example, they should be filling in the same template which enforces data integrity (eg required fields and allowed values). Don’t allow anyone to roll their own. Standardize everything. At that point your job becomes pretty easy with solutions ranging from converting the data to CSVs or just uploading it to a sql database (eg mysql) with some gui.
I would recommend thinking pretty hard about whether there is a business value in limiting access to data that people “don’t need.” While it does make sense for reporting to have simplified views, managing user level access to specific subsets of data is often not justified for the level of effort required. If you’re dealing with actual (eg government) classified information or if there are highly valuable trade secrets that need protecting, that’s another story. But if it’s just “Jeff in NY doesn’t need to see Jane LA’s sales numbers,” it’s probably a waste of effort and will be a time and money sink. I’m saying that as someone who has worked on very highly classified systems.
Anyway, everything you’re talking about is a solved problem That can be solved using excel and maybe an off the shelf database that an intern could set up for you.