Can't transfer iBooks pdfs from first gen iPad to new MacBook Pro

I have a bunch of important pdf files on a first gen iPad (iOS 5.1.1) that I want to transfer to iBooks in a 13" MacBook Retina.
In iTunes, choosing Devices >Transfer Purchases from My iPad isn't moving them over. I've been able to transfer all the non iBooks pdfs from GoodReader, etc. In iTunes, I can see them in the Books section of "On This iPad" but can't do anything but view info.
In iBooks, choosing File >Move Books from iTunes isn't doing it either.
Syncing warns me that it's going to delete the iPad files.
I'd rather not pay for 3rd party software if I can avoid it.
Thanks.

No they're not in the iTunes library. Purchased titles transferred and a few other things but a bunch of DRM-free pdfs and DRM-free EPUBS won't Budge.
"Or you don't see them with the iPad connected to the Mac, with iTunes running, the iPad selected under devices and then look in the books tab of iTunes on the right?"...
No. However, if I go a couple tabs further to the right, to "On This iPad" and select Books in the left column, they're all listed. I just can't do anything but view their info or rate them.

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