It's hard to be sure from a distance, but it looks like your problems are a mix of duplicates, corrupted files, perhaps protected iTunes files, I am not sure.
I think for now you are taking good first steps in figuring out what's what.
If Amazon or iTunes files pose specific issues, I don't know much about those.
Converting file formats can sometimes help in the sense that the converter will rewrite a file (it's metadata) with a clean slate.
(but if the audio stream itself is corrupted it will not solve that)
Also understand that converting from a lossy format to another lossy format will affect the sound quality and diminish it.
Duplicate music files could (to a limited extend) be handled by MusicBee, but there are also 3rd party tools that can help in finding possible duplicate files on your drives.
Corrupted files will be much more difficult to determine. But crazy filenames and extensions will surely make them suspects.
If your old iTunes and Amazon files are valuable to you, try to backup everything you have on a separate drive first.
Then you can always have a second try when things go wrong.
Maybe other members can relate to the issues as described and contribute with some other suggestions?