Some success.
Joboshare iPhone iBooks Transfer at
http://www.joboshare.com/iphone-ibooks-transfer.html
Seems to be doing the job. But no guarantees.
At least it shows the correct titles for 1136 of my books leaving out of 1736.
I am currently downloading all these to my PC.
Slow.
UPDATE
Bought a copy as the free copy is limited to 99 files.
Downloading my books is going well.
Has downloaded all epubs and pdfs which were loaded in iBooks.
Next I will download all my music.
I am very happy with this!
UPDATE 2
It is downloading all my music from my iPod.