I think I have a handle on what's going on now. It appears that iTunes (for some reason) cloned (i.e. made multiple copies) of about 4 free books that I got from the iBooks store.
I started looking at these because iBooks and book loading errors are what I was normally seeing.
While digging around I found that when iTunes downloaded the books it copied them to not only the iTunes Media\Books folder, but also copied them to iTunes Media\Author folder.
After going through and deleting the books I'm now able to complete a sync on my iPhone. I'm trying out the iPad now. It seems that when iTunes sync receives an error on a sync it considers everything from that point forward in the sync process to be in error and just kinda haphazardly stops where it's at. This makes it impossible to complete a backup and maddening when doing a recovery.