Backup to iTunes, connect ipad 4 to iTunes, restore.

This is what I know.

As long as those files e.g pdf, ppt are inside your apps for e.g Adode Reader, backup backs-up even the files inside. At least that is how I think my previous backup worked.

Take a look at this http://support.apple.com/kb/HT1766

"Backed-up information includes purchased music, TV shows, apps, and books*; photos and video in the Camera Roll; device settings (for example, Phone Favorites, Wallpaper, and Mail, Contacts, Calendar accounts); app data;"

I believe "app data" is what you're talking about.

And take a look here for more manual work. http://lifehacker.com/5891964/can-i-transf...e-to-a-new-ipad