I have said this before and I know I'm going to get commnets about it. If you want all the duplicates, syncing problems, iTunes deleting music from the hard drive, missing music, missing artwork etc etc to go away MANAGE ALL YOUR OWN MUSIC.
Turn off all itunes assistance, keep the iTunes music library empty (where you can) make you own music library folder and import that.
I started down this path over two years ago.
Number of duplicates installed by iTunes 0
Number of songs missing 0
Number of Artwork missing 0
Number of Albums mixed up 0
Number of songs deleted from iPod or hard drive 0
Number of Exclaimation marks 0
iTunes is a great program, but it is after all a computer program, if you want it to manage you instead of you managing it that's fine. Again I have said this time and time again, nearly all the people on this forum that have the problems listed above are letting iTunes manage and organise their libraries. If you take control of it yourself these issues will go away.