[Question] Transfer iBooks files (non-purchased) to PC

[shyam09]

So in lieu of the recent update on the iOS 6.1 jailbreak coming soon, I've started to back things up to my PC. Is there any way I can back up the files from iBooks? These are epubs and pdfs that i transferred from my computer. I recently did a clean install to windows 8, so I'm sure if I do some digging I will find most, but I want to know if there is a way to back up iBooks?
Maybe a 3rd Party software. since iTunes isn't helping me (I'm currently doing a "transfer purchases" to save all my apps to my PC, but I can't sync books because I get the warning that everything will be erased.

Also, to back up the data from other apps (for example iAnnotate, I just go to "Apps" in iTunes, and go under "File Sharing" , select IAnnotate, and drag the files to a place on my computer (ie. desktop or a folder). Or is there an easier way to do this?

Extra Info:
OS: Win 8 Pro (MC edition)
iPad 3,
iTunes 11

EDIT: nvm, i got DiskAid for free (university email), and i just used that.