I have managed to do this via rename - kind of. Instead of renaming the parent folder, a new subfolder is created and files are moved into it. That works, so long as there is an easy way to then push all those new folders up a level...
It works for the first track in a directory, but when it gets to the second, it gives me an error saying that the filename already exists. I guess it's trying to create the folder again?
Come to think of it, doing things this way would mean I still have to manually move my cover art. Maybe I'll just go through and change the numbers by hand, it'll only take an hour...