John -
Most simply, listing documents should be possible with either the documents shortcode, or via the /documents/ archive. The same goes for the document_revisions shortcode for each documents revisions.
More broadly, if you don't mind getting your hands a bit dirty, get_documents() and get_document_revisions() should be exposed in the global scope, and should work just like get_posts().
On all of these, see the plugin FAQ in the wiki (and feel free to contribute if it's unclear).
As for comments, there's no reason they wouldn't work almost entirely natively. The only issue would be the UI. As it is right now, there's no "document" page. It simply serves the file. You'd have to build a comment form that would associate the comment with the document, and it should work just as any other comment would (documents are posts with no template).
Hope that helps,
- Ben