Ok folks .. here is the solution that has finally worked for me. After spending over 45 days on and off the phone with Apple support, this is the work around solution for the ibooks.
Set your IPAD as new and go through that whole set up process. Plug in your device so it can communicate with iTunes. When you load your books from iTunes to the IPAD do not synic the first time. You will have to drag and drop from iTunes the books/music you want loaded. After you manually do this, the synic seems to work fine.
Also things I have found. By dragging and dropping the volume of books I have. It took less time to load on my IPAD then it did trying to synic and waiting over 24 hours to load in IPAD (at which time you can't touch your device). It was during this huge file load that the Ibooks App/iTunes/Cloud and whatever other Apple software all talk, that the books being loaded start to go squirrely and go into limbo.
Here is the problem. When you get the message "waiting for files to copy", itunes and your device are having an issue. So files that iTunes thinks it has copied over, actually go into limbo and sit there greyed out and won't work on your device. When you try to re-synic again, iTunes says "hey! I have already copied these over" and will sit there on "waiting for files to copy".
A way to fix the files that are in limbo, delete your app and re-download it. The files that moved over from iTunes to your device will still be there, however, the files that are in limbo will disappear. This should stop the synic issue ... or it will identify that there are issues with some of your files.
Is this a great fix ... nope! I pushed and pushed to be allowed to talk with someone from DEV and got stonewalled. I even brought in their Customer Support from Corp Head office and got absolutely no where.
BOTTOM LINE: iTunes and your devices can not handle a huge transfer of files from iTunes to the device and it creates this limbo "waiting for files to be copied". I find this ironic, because I have never had this problem when it comes to my music (transfering from iTunes to my IPOD), however, I haven't synic that device in awhile, guess i am scared it will do the same crap.
I also got Apple to acknowledge that when they test out their new software upgrades and devices that they ONLY test with iTunes Store only products (ie: music/books/apps). Infact, Apple DOES NOT test any outside source materials. I found this rather pathethically sad, since 99.9% of the users of any devices get their music/books from sources OTHER then the Apple Store. This means that a file that USED to work for you (example: a song) and was loaded on your device fine before all these software upgrades in Nov/2013 might not work anymore because of a change they have made in their software.
Last conversation I had with Apple (both Support and Customer Service) was them telling me that DEV was looking into the problem but did not have an ETA on when a fix would happen.
Also keep in mind, I found that even with a 128kg AIR, it doesn't like to hang alot of books. I found that at around 3k in books, the device starts to freeze up. This contradicts the Apple concept, that the device can hold as many songs/books as you want, until you reach the max room available on the device. I can clearly tell you this statement is infact false. The device does not like to hold that many files and it starts to delay on you (quite noticeable) at 3k.
So, that in a nutshell has been my experience with Apple Support. 45 days later, I have reset my Air 10 times, tried to load all my books (at one time) 9 times, to finally find that the only way to get them in was a drag and drop the alphabetic (one letter at a time) and let it load on the IPAD before I would drag and drop more. The synic problem doesnt happen anymore, I had to eliminate 2 books that itunes just would not send over to the IPAD even though there was nothing wrong with the file. Am I happy? NOPE ... talk about bait and switch.
Consumers beware ... Apple doesn't necessarily deliver what it says it will.