Apple - Transferring PDFs from iBooks to your laptop/desktop

Grab a copy of iExplorer (freeware), connect your phone, open iExplorer, select your device, and navigate to Media > Books. All your PDFs should be there.
However they all have cryptic names and there's no QuickLook in iExplorer, so you need to copy them all and then look which ones you need.

Even though you've already solved it, I transfer in between my iPad/iPhone with Dropbox. I usually buy a lot of books on my iMac that are epub or pdf that aren't in iBooks, so the quickest way to transfer them and keep them backed up is in my dropbox. When you install the app on your phone, you can navigate to a book and select "Open in iBooks". It's a really handy way to transfer things in between the devices.

Why not select share from the document in iBooks, then send it to yourself by email, then the attachment can be downloaded onto any computer from your email?