Well, one suggestion I do have is that if the missing tracks are in your Library, but on a different album, you could try creating Playlists for the albums.
For example, say the album in question (album A.) has a track missing from it, but that song appears on another album in your Library (album B.). Create a Regular Playlist which has all the songs from album (A.) that are in your Library and also the missing song from album (B.). Move the songs to the correct sequence order as they were on the original album and give the Playlist the name of the album (if you wish). Put that Playlist into a Playlist Folder named ALBUMS - COMPLETE (again, only if you prefer. You can name these lists anything you wish).
Okay, you have to remember that some of your albums only have all the songs in the Playlists, but it saves space on the iPod and duplication in the Library.
I've had a similar problem when I have all the songs from one album, but on different compilation or "greatest hits" albums. By giving the Playlist Folder a name in all capitals, it stands out so I know instantly that it's the one I'm after. On some older iPods, it was not possible to differentiate between Playlist Folders and Playlists. By putting the folder names in capitals, I know there are additional Playlists in the folder. Look at my screenshot below, but before you do, note the following:
In iTunes, Playlists are shown in alphabetical order, but in the following sequence;
- Playlist Folders
- Smart Playlists(within the folder)
- Regular Playlists(within the folder)
- Smart Playlists
- Regular Playlists
But on older iPods (such as the Classic), all three (folders, smart and regular playlists) are shown in strict alphabetical order, so capitals was the way to remind me which was which. On the latest iPod Touch, all three are still in strict alphabetical order but the Playlist icon indicates which of the three it is.

In the screenshot you will notice a Playlist Folder named ALBUMS - COMPLETE, a second Playlist Folder named ARCHIVED PODCASTS - NO SHUFFLE and a third folder named GENRE. The capitals tell me there are Playlists in them. In my first folder, you can see three albums, the Mungo Jerry, Parliament and Third World. Ignoring my personal choice in music 😁, in each case the songs from the original album are scattered across different albums, but the Playlists allow me to play them as they should be without duplicating any song unnecessarily.
My second folder should be self-explanatory. You may wonder why I need the third folder - GENRE, which you will notice has two Smart Playlists and one Regular Playlist. The reason for it is so that I can assign two genres to one song, something which is not ordinarily possible.
For example, if I want a song in "a genre" to be listed along with the Acid Jazz genre, I add the text "Acid Jazz" to the Grouping field of the song and the Smart Playlist picks up all songs with the genre Acid Jazz and any song with the words "Acid Jazz" in the Grouping. The Chillout Plus list is similar. The Christmas one is just Christmas songs.
A long answer, but hopefully, it gives you some ideas.