Hey, Apple is everywhere, right?
iTunes can be a pain to set up, and I've spent hours on it as if I were tinkering with an old car. What I'd recommend after disallowing iTunes to manage the library:
1) Get the music folders and files all organized, since this is how iTunes should read them from now on.
2) Select "Add Folder to Library" and bring them back to iTunes. The tags should be the same, only iTunes will point pack to the location from which the songs were added.
3) If you haven't deleted the existing songs, you could either do that, or use the search field (top right) to narrow down the culprits. Then you can arrange by "Date Added" (the view option should be present, and if not, View > View Options > Date Added) and delete the older, misaligned songs.
Hope that helps.