Itunes not syncing new songs + other problems. Help please!

My computer had to be taken to the shop last week and the whole system had to be wiped and recovered. I forgot to tell them there was another file I wanted saved so I lost a lot of my music.
I managed to download the free version of touchcopy and get my music back on to itunes. The music that I lost comes up with a question mark and wont play on itunes but is in ipod and plays fine. Is there anyway I can get the original files of these songs on to my computer as I cant make playlists or anything with these songs?
Also in my ipod a few of the playlists have been screwed up and there are about 5-6 versions of 90s music, recently added etc that have nothing in them. Is there anyway to get rid of them?
My main problem now is that itunes wont sync the new music that Ive just added (it wasnt on the ipod before). When i plug my ipod into my computer itunes tells me "sync is complete" and it also shows up with "do not disconnect" on my computer even though the sync is apparantly complete. How do I sync this music on to my ipod??
Sorry for that incredibly long winded problem, I really hope someone can help me!!

Here are things I did:
Unchecked the playlists, Synced to remove all songs, rechecked them, synced again. NO RESULT
Added the songs manually by dragging and dropping them into my iphone. NO RESULT
Eventually, I cracked, and went for a restore, which luckily did the trick.
No solution was found however, and I would love to know if anyone has encountered this issue as I'm sure it will happen again.
Thanks

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