The ‘root directory’ is where you open up your player in Windows Explorer (preferably in MSC mode) and see the folders Music, Recordings, Playlists, Sport, Audiobooks, etc. and a few files. This is your root (or top) directory. Manually drag & drop (or copy & paste) the unzipped .bin (firmware) file here, but not in any on the folders; just aim for a blank space and release your mouse button.
Having said that though, I don’t think this is your problem. I would suspect that it lies somewhere with one (or more) of your files. Try sending a few over at a time, up-plug and see if they transfer OK. If and when it hangs up again, you know your problem child is in that bunch. 
Let us know if you have any other problems.
