Hi Chris,
I'm not entirely sure what kind of help you were looking for, but this sounds very doable with DMX.
I am setting up a portal with a lot of files (10,000+) and 50+ different user types who would require restricted access to their own individual folders.
Check out the documentation on "Root Pattern" in the module settings help file.
I've also got to deal with 10+ different pages on the site which require their own document modules accessing a different subset of files.
DMX is very sell suited to this. You add the module to the page and set the root folder to the correct place in the folder/file tree (module settings).
Peter