View Duplicates
Not sure if this will help, but in iTunes click Music in library, then click the View menu option, then click Show Duplicates. Now click the column heading for Kind to sort by Kind. All AAC files will be grouped together. The unconverted files will also be together. Again, this view only shows duplicates. Next, click the first unconverted duplicate (I'm guessing MPEG's), now after scrolling to the bottom of the files you wish to delete, hold the Shift key down and click the last file. This should how have highlighted all the files you want to delete. Hit the delete key and answer the prompt as to whether or not to keep the actual files or send them to the trash can.
To be safe, you may want to simply Uncheck the selection so they will not be on your iPod, keeping them in your library for other uses, such as cell phones.