Sending 160gb iPod content back onto mac

About 6 weeks ago I had to reinstall Lion OSX on my mac I didn't have a time machine back up and lost everything so I went and bought touchcopy for my mac. I have a 160gb iPod that is almost full so I began the process of transferring all my content from my iPod back to my mac this took forever because every so often the program kept stalling so I would have to start again several times which has resulted in doubles, triples or even quadruples in some cases of certain songs which clogged up my hardrive because I only have 146gb of music on my iPod but when the transfer from my iPod to mac finally completed it's now saying that I have 220gb of audio on the computer. But of course the doubles and triples of tracks don't show up in iTunes because that would just make things too easy.
So I used Omni Disk sweeper to locate where all these extra files where it said they were in iTunes so I just spent about the last 3 and half weeks individually going through each artist and album and deleting all the duplicates only the the songs that had 1,2 or 3 next to it not the originals (I have 394 different artists saved on my iPod so this has been an extremely tedious and painsteaking process) so finally today I finished and had hoped this would be the end of this nightmare only to discover yet another problem. Now when I click on certain songs it keeps says the files cannot be located even though if I go through Omni Disk Sweeper I can clearly see the original files is still there yet itunes keeps saying it can't locate it.
So please can somebody help me because I am at my wits end at this stage I just feel like throwing iPod and computer out the window I have been more than patient with this and have tried everything and still I am getting constant problems. Their has to be some easy solution to this problem. I have had to to reinstall before and reup all my music from my iPod to my computer but I have never experienced this amount of problems or difficulty before as I am sure anyone who's been through it knows it's extremely frustrating. I have a 146gb of audio on my iPod some of which is rare live stuff that I will not be able to get again so starting over is not an option I would just stop using MP3 players alltogether rather than do that. I already tried contacting apple but because my music is from my own cds or bandcamp downloads they can't help me.
So please can somebody help me before I lose it.

Yeah, syncing them will wipe the iPod. You need an iPod Manager (other than iTunes) that'll move songs from the iPod to the Mac (which iTunes is design not to do).
http://en.wikipedia.org/wiki/Comparisonof_iPodManagers
I used iPodRip. It took a little finaggling (sp?) so next time I'll try something else. You might want to look up some reviews of the others and see what'll work for you. Some save the play count history & playlist, others don't.
Anyway, it's doable.

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