How can I transfer my iPad iBooks to iTunes library?

I'm having a problem getting my iPad books into my mac and I really could use some help. The situation is, my mac got stolen a few months ago and I finally could get a new one. I also have an iPad, where I had thankfully stored all my iBooks. They're backuped to iCloud cause I could restore them to said iPad (using iOS 6) just using my Apple id. But most of them weren't bought at the iTunes store but downloaded from other places. The only thing I can see in iTunes (v. 11.0.2) when I connect the iPad is the ones I bought at the iTunes Store. How do I do to get my old ones in iTunes and (now that I know how hard this is) in my mac to do another backup somewhere else than in iCloud?

Has someone done this before and could help me? I've been looking for it for hours and I can't seem to find a solution. I'd be very grateful if someone could point me out in the right direction. I mean, they're there! How do I get them? Help!