If they are on your computer then have you tried either doing File > Add File To Library in iTunes or just dragging them over and onto iTunes . If they are supported by iTunes then they should then appear in the Books section of your iTunes library (if Books doesn't show then you can tick it on the General tab in Edit > Preferences). You should then be able to add/sync them to the iPad via it's Books tab when connected to your computer's iTunes.
1) Today Itunes prompted me to update the OS on the IPAD.
2) It warned me to back up IPAD before I did. I did
3) I updated software.
4) It returned with an error saying it could not install software and I must restore to facotry settings
5) I resotored to factory settings
6) After that I attempted to restore contents of my IPAD from Itunes on my Windows 7 machine.
7) It restored only music but no applications and no other information
8) I spent all day on the phone with Apple Support who managed to get the applications restored by going through one by one and syncing.
9) It took a few hours
10) After I finished I noticed that files/documents associated with various applications like Kindle, Goodreader, Penultimate Notes were missing on the IPAD.
11) I have made a few phone calls to Apple and thy claim the following: "Apple is not responsible for restoring files or data associated with any applications, only the application itself. It is your responsibility to contact the application developer to get your files restored." This sounds patently absurd to me. I spent half an hour explaining the absurdity of this claim to the Apple representatives but they are firm and non-wavering in this opinion. One even claimed that restoring does not restore applications which of course is not correct.
12) I gave them the example of MS Word on MacBook Pro. If I save/back up on another machine and then restore back to the original machine I would expect to be able to see the Word files I had created and saved. That in particular the failure to view them would not be Microsoft's responsibility but Apple's. They disagreed saying it would be between me and Microsoft and the Apple devices had nothign to do with saving or successful restoring.
13) So I have lost all e-books purchased on Kindle, plus all documents saved on Goodreader application, notebooks on Penultimate applications, and my children’s drawings on their drawing applications. Apple Support say I should contact each application vendor to try and recover the missing data. They refuse to tell me how to get it from ITUNES backup stored on my Windows 7 machine as they say it will not be there.
They have asked me to write to
Apple Customer Support,
quoting case number 319718819.
I had exactly the same experience. Regardless of who supports the applications, the backup feature in iTunes for the iPad states "full backup". What other vendor would state they are doing a full backup but not back up your data.
I was almost ready to buy a Mac Air before this restore disaster happened. I bought the Dell Ubunutu Laptop instead which is much more powerfull and just as pretty.
After restoring from iCloud backup of my old iPad on my new iPad I've seen no books or pdfs in iBooks as everybody else. I went to Settings => iBooks and turned on Sync Bookmarks and Sync Collections. In a matter of 2-3 minutes I got all of my books and pdfs back. It looks like it was downloaded from iCloud, since WiFi on my old iPad was turned off at the moment, so it was a single device sync with the cloud, not syncing 2 devices being on one network.
I have no idea why Apple didn't keep this setting on by default.