How can I transfer iBooks from my 4th to 5th gen iPod Touch both running iOS 6, using iTunes 11?

Question

I downloaded the e-book The 80/10/10 Diet by Dr. Douglas Graham directly onto my old 4th gen iPod Touch from interviewthemasters.com a while back so my Purchases in iTunes 11 still shows no books available to re-download.  _None_ of my iBooks content (e.g. bus route PDFs) show up _or_ seem to sync, even though I have Settings that all available apps sync their data _and_ back up into iCloud.  I even got to a PC, downloaded iTunes, restored from my 4th gen's backup right onto my 5th gen, and still nothing in the way of my iBooks content, though the first time I pulled it up, I saw them on the shelf for a split second...>:-|  What's going on?  Why won't it propagate to my new device via iCloud?  Nor can I find a way through iTunes 11 to get my content to my new iPod (yes, I have all authorized under the same Apple ID).  Please help!  All my annotations through iBooks are very valuable to me and I don't want to keep my old iPod and drag it out any time I want to reference my own notes on a book I bought!  Am I to believe Apple cares nothing for my personal data unless it's through their store, and extends entertainment industry shenanigans to disable their own apps with _my_ content garnered elsewhere, _presuming_ it "must" be content which can be found on the store?!  If so, how do I get control back of my own data?  Apple used to say "tough" if you wanted to re-download purchases.  Are personal effects like Notes and iBooks still a drop-stitch?  The larger issue of ignoring private content and disabling their ecosystem presuming content is illicit outside their store is pernicious to say the least, and if Apple officially declines to right that wrong I really will leave their ecosystem, and burn the path behind me.  I can't be the only person in this boat regarding cavalier ineptitude/negligence regarding basic functionality other than hooked into Apple's money machine.

Answer 1

To reiterate, the 80/10/10 book was purchased from interviewthemasters.com and worked perfectly as a e-book through iBooks including annotations, hilighting, etc.  It never syncs to my machine _or_ iCloud, so I cannot try your recommendation regarding the iTunes Book library, unless you can explain how to get it from my iPod into iTunes.  The fact Apple syncs only its store's content and disables syncing for my own independently procured content, particularly as the sole means of communicating with iPods, I find reprehensible and is a perfect example of screwing their customers and hobbling their devices for the supposed privilege of offering entertainment industry content since offered elsewhere far less restrictively and at higher quality (Spotify, anyone?).  In any case, if anyone can explain how I can get my own book onto a different iPod, I'd love to hear from you—and no, I'm not anxious to use shady PC utilities, and those well-reviewed don't support anything but music and movies.  I do not have access to a Mac, only my iPods and a PC, right now (I'm working on it!  Trust me, aside from wholly unnecessary shenanigans, Apple offers a vastly superior product!).