I am not using iPhoto on this old machine. So I have a hole in how I keep backups of photos. I'll have to look at that later. It is highly recommended that anyone upgrading iOS make sure that they have a full backup of photos.
I do not have room for my media (photos, iBooks, iTunes) on the local drive, and so have it on an external drive. I moved the drive from one machine to another, and never migrated iBooks. Now I have to look for them and update anything that needs updating so that I can again sync iBooks. Note that audiobooks are still in iTunes - no problems there. But once iBooks became an app for Macs, iBooks were no longer in iTunes.
I have my iBooks on my Mavericks-based machine. Where?
So I copied files from my Mavericks computer to a location available to my iTunes server computer. I tried to import them. It turns out I had some of the files located on my old Lion-based iTunes machine, so I deleted duplicates. I tried to sync my iPhone. It said it could not locate some files. I ended up deleting ALL iBooks from my iTunes library, unselected all books from sharing with my iPhone, and then reimported the whole list in the shared location. I still had no PDFs; importing PDFs did not work. I had to drag and drop the PDFs into iTunes in my old iTunes server. I then selected books (and PDFs) to sync, and it all worked. Whew.
The good thing is that I had put some PDFs into categories in iBooks on my iPhone and iPad. They fell right back into those categories once re-synced even after all of my cleanup shenanigans. I did not have to re-select the 15 PDFs related to a class I took into a category for that class.