iPad: How to sync/backup notes and highlights from a PDF/epub read on iBooks?

Question

For books purchased on the iBooks store, it seems that notes and highlights are automatically synced with Apple's servers.

My problem is that I read quite a lot of PDFs or epub files which were not purchased on the iBooks store, and rather manually copied to the iPad via iTunes.

Is there any way I can sync/backup my "precious" notes and highlights to either some online service or directly to my Mac?

Any solution would be most welcome, even if it involves SSHing into the JBed iPad or what not.

Thanks!