Dylan,
File management is something different than document management. What you want is logically impossible. DMX is much more advanced than the modules you mention. For a start it has a much more fine-grained permissions model. This can never be matched with the modules you mention. Whatever you end up programming for this, it will end in disaster.
Peter

Okay - can you maybe suggest how I could do something like what I mention?

Heres what I was thinking - Each week somehow syncronize the files in the site and in DMX and then let IIS reindex them. This method seems to lose all the benefits of versioning, categories, and descriptions. Unless you can sugesst someway to keep those elements when reimporting in the directories from the portal.

This might be a total loss if I cant figure out someway to handle this

A second thought maybe the places where I use the documents module I should use DMX instead so files are uploaded through it and not into the regular file system.

Dylan,
You're obviously going to have to compromise somewhere for the reasons I mentioned above (file mgt <> doc mgt). Having said that there are some ways forward. To present a file through text/html can be achieved through overriding the screen that displays a file in DMX for this file type. Now, like for all file types, ViewDetails.ascx is shown. You can set that to a custom screen that actually reads the contents and display it. There will be an add-on for DMX available to do this soon. The second aspect is synchronization. This is a lot more difficult as you don't have version mgt on a hard disk (this is one clear example of file mgt <> doc mgt). DMX uses obfuscated names in part to avoid name clashes (in versions). You can match the new to the original filename in the DMX_Entries table. How you solve the versions issue is up to you. You also need to solve adding a new item from disk to DMX. This includes how to set permissions (I'd suggest inherit from parent).
If all you need is to present the files (i.e. you don't need the docs module per se), then you can also check out the ShortList add-on that shows a single DMX collection somewhere for you.
Peter