Help Clean Up my iTunes

I use an external hard drive to store all of my iTunes data.  Recently, I was getting worried that it may crash, so I bought a new hard drive.  While making the switch, I decided it was time to clean everything up and start fresh. So....
What I've been doing is unchecking all of my duplicates.  Next, I plan on cleaning up the tracks/artists and everything to it says what it needs to and everything will look very nice on my iPod.  I have to do all of this manually, since I listen to non-mainstream music (mostly jambands that I've accumulated randomly).  When I'm done with that, I will delete my unchecked songs. 
My question is this:  I was wondering if it would be good to back up my iTunes library, once everything is clean and exactly like I want.  Then, I want to delete everything from iTunes, delete the 'iTunes' folder on my hard drive, and then copy the backup back to it.  This way, not only iTunes is clean looking, but so is the iTunes folder on my hard drive.   Is this overkill?  The main reason I want to delete the cluttered folders is because I don't want two folders of essentially the same things taking up twice as much space as they need to.  I have over 100 Gigs of music, and growing, so please give me any advice you think is helpful, even if it goes against what I'm asking here.  It's time to get my music organized, and I could use some help.
Thank You-

Hello there, SharmagneChampagne.
The following Knowledge Base article  has extensive steps for an iPod not being recognized:
iPod not recognized in 'My Computer' and in iTunes for Windows
http://support.apple.com/kb/TS1369
Thanks for reaching out to Apple Support Communities.
Cheers,
Pedro D.

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