Wasn't meant to be any undertone. 🙂
I obviously don't know what you have and haven't read before you posted, but I may have assumed from your second post that you hadn't really looked at my first one. Apologies for that.
Anyway, the checkmarks don't have any other purpose in the show duplicates display from normal. though I guess one could use them to mark things out in that display if one wanted to, then delete later using a smart playlist of unchecked tracks.
The deduper script arose from a conversation about the difficulties of mechanically deciding which tracks should and should not be removed by any automatic system. It isn't completely perfect because it can only detect tracks with the same metadata, not the same audio data, but I think it beats working by hand.
One of the issues with duplicates is when two entries in the library are connected to the same physical file. In the background thread I have termed these logical duplicates. Deleting either entry and the underlying file breaks the remaining entry in the library because there was only really one file to start with.
On the other hand if you are trying to recover wasted space taken up by physical duplicates on your drive then it isn't enough to simply remove them from iTunes without trashing the files related to the copy you remove. You will tidy up the interface in iTunes, but won't recover any space.
There is a tool called iTunes Folder Watch which can be used to scan the media folder and can tell you which files in the media folder are not connected to the library and (with the option check for dead tracks on start up enabled) which entries in iTunes are not connected to any file. If you reconnect everything in your media folder to iTunes (you could also just use File > Add Folder to Library for this) then my script should be able to safely dedupe and recycle where appropriate.
I cannot understate the usefulness of a complete backup before you start. I recommend you purchase a second external hard drive and backup using the method suggested in Backup your iTunes for Windows library with SyncToy.
When you have cleaned the duplicates from your library there is more advice at Grouping tracks into albums on organizing it to the best effect for an iPod classic. In particular it doesn't group on album artist, so any albums that have guest/featured artists may break up or repeat on the iPod even when all looks well in iTunes.
Regarding the files with exclamation marks. The "missing file" error happens if the file is no longer where iTunes expects to find it. Possible causes are that you or some third party tool has moved, renamed or deleted the file, one of its parent folders, or the drive it lives on has had a change of drive letter. It is also possible that iTunes has changed from expecting the files to be in the pre-iTunes 9 layout to post-iTunes 9 layout, or vice-versa, and so is looking in slightly the wrong place.
Select a track with an exclamation mark, use Ctrl-I to Get Info, then click No when asked to try to locate the track. (Due to a bug in iTunes 12 you currently have to say No twice!) Look on the summary tab for the location that iTunes thinks the file should be. Now take a look around your hard drive(s). Hopefully you can locate the track in question. If a section of your library has simply been moved, a folder renamed, or a drive letter has changed, it should be possible to reverse the actions. If the difference between the two paths is an additional Music folder in one path then this is a layout issue. I can explain further if that is the case.
In some cases iTunes may be able to repair itself if you go through the same steps with Get Info but this time click Locate and browse to the lost track. It may then offer to attempt to automatically fix other broken links.
If another application like Windows Media Player has moved/renamed the files then the chances are that subtle differences in naming strategies will make it hard to restore the media to the precise path that iTunes is expecting. In such cases, as long as the missing files can be found somewhere, you should be able to use my FindTracks script to reconnect them to iTunes. See this post for an explanation of how it works.
If the files have been deleted then you will need to rerip or redownload from source.
tt2