Restructure iTunes Library File Hierarchy
Have used Itunes for about 10 years now.   Keep you backups, but switch to the setting "Keep Itunes media folder organised" in the Settings.  At the same time I always check "Copy Files to Itunes Media folder when adding to Library".

Itunes sorts music per artist by default.   right clicking on any item can take you to the physical spot in you library.  Get over the apprehension and just edit the metadata.  

To get any music referenced by your library follow steps at http://support.apple.com/kb/ph1459.

After that all the your stuff should be in you ITunes library.