I am trying to introduce more and more Mediawiki in my company.
Welcome to the club.
# Links (usually nasty file:// links) does not work with URL containing spaces
Try encoding the space char with "%20" (e.g. "file/////MyServer/My%20Folder/MyFile.odp"). Not sure about this though.
# Is there a plug-in to scan documents like .PDF or .DOC on the fly during the upload to index them in the search engine?
Look at the recent thread on "Storing or Linking Documents". Quoting Rob from there: "I've thrown some very experimental initial work on such an extension into Subversion; trunk/extensions/FileSearch" But there might be more info in that thread.
As for the rest (partial match search, auto-backup), I don't really know much about those issues.
HTH.
-- F.