Why won't iBooks wirelessly sync epubs or PDFs to my iPad?
I don't know if you still need this issued solved, but I struggled a lot to sync my ePubs (not bought through Apple) between my Apple Devices.

Here is the solution I've come up with (This can be done on both OSX or iOS):


Save your ePub/PDF file on iCloud Drive (inside a folder, just for organizational purposes);
Then open that file from the iCloud Drive folder into iBooks.


This way, the instance  of your ePub/PDF will be the same running on both your iDevice iBooks and your Mac iBooks. 

All changes that you make (add bookmarks, highlights and current page) will also sync.

Regarding your collections, they will behave as they should syncing normally between devices.