I have had the same error 54 issue appear recently. Following the advice from experts here, I tried a few simple procedures -restarting, using the disk utility- to no avail, until thinking about some hints also here, I realised I had never used iBooks in my MacBook, just in my iPad, so I just logged in to iBooks in my MacBook, repeated the iPad sync-ing procedure and the issue disappeared!! The conclusion in my case is rather obvious, the logging-in procedure I describe seems to be a requirement for a correct sync, but what I do not understand is why this error only appeared for the last two weeks or so. The only difference I can think of is that I have been archiving quite a lot of PDFs in my iPad iBook Library recently. This is written in the hope that it may help others not very much computer-literate as I am, the same way that -quite by chance- it helped me.