iCloud removes my third-party ePubs and PDFs from my iPad without permission — how do I stop this? I had to pawn my iPad for a bit, so I uploaded all of my third-party books to iCloud and of course, when I turned iCloud off, the material was removed from the device. Now that I have it back I naturally want to download my entire library to my device again. At first it let me download about half of my library, but when I tried to download any more, suddenly all of my books were pulled back onto the Cloud. I assumed it was a storage issue, and gave myself another gigabyte of space... NOW, not only did the problem continue but it’s actually gotten worse: iCloud periodically pulls back any book I try to download. It doesn’t even notify me, let alone asks permission — it just does it and the cloud symbol suddenly appears.  

Is there some setting I got jacked up or what?
It sounds like you have "Automatically Manage Storage" turned on in the preferences. If the device is almost filled up, then iOS could be deleting iBooks that are available from your iCloud account from the device.

You can re-download them from iCloud when needed. Bookmarks, placemarks, etc. are also saved into iCloud.