I have updated to iOS 6. All my files were lost. Help!

Hello Fine Gentlemen!
I am sorry to borrow your time, but this problem has made me mad recently. I have an iPad 3rd Gen, which I could no update (somehow) with the iPad itself. The same with my Mac. I kept getting error messages (although no code though, so I am unable to search them by myself) so I decided to do the update on a different Mac. I had backups everywhere.
When I updated it on the other Mac, the iPad went into recovery mode. It updated, but as soon as I lifted my iPad, there was nothing. Restore from backup did not help either. Only the photos were recovered. But my apps and it's data, all gone! Now you see, this is curious, because for example, I lost all my files on iBooks (PDF's) and I have no way of retrieving them, still, only one I was able to download it again on my iPad through the Dropbox app. Nevertheless, when I opened the PDF, the iPad remebered where I have last left the PDF, and it opened in the exact page I left it.
This does give me hope though. It seems the app data is stored somewhere, only I don't know where.
Could you, my dearest Apple users, will you be able to solve the Enigma?
Yours Sincerely,
The King.

I have exactly the same issue since iOS6 upgrade ona 4S - 3G not working at all, Wifi is OK though. Major own goal by Apple here I think...:(

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