Why won't iTunes let me manually sync PDFs to iBooks?

Solution 1:

You can get the PDF's on your iPad via some other method (e.g. Email, DropBox, etc.) and then choose to open the PDF inside iBooks.

Solution 2:

Try the following:

1. Sync your iPad
2. Drag your PDF (from Finder) into the LIBRARY section, left panel uppermost section in iTunes
3. It should then show up in your Books category in your LIBRARY
4. With your iPad connected drag the desired PDF from the Books category in your LIBRARY onto DEVICES/Your iPad
5. iTunes should display something like Updating Files on ... and Copying 1 of ...
6. Your PDF should show up in iBooks in the PDFs bookshelf section

Note: For me this only worked using a USB cable - NOT by WiFi (for whatever reason...)