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Do it through iTunes. Before you start, make sure you have iBooks on your iPad (free download)
Drag the book to your iPad in the left sidebar of iTunes, and the book will be available in iBooks.
Quit iTunes and look for the "old" library. It should be somewhere in C:\Users\your username\Music. Make sure the files that used to be there are still there.
Second thought: you didn't copy the old library, but certainly created a new one? That's an important note in my link.
Thanks Johanna, I have found the original library now and have loaded the books.
Thanks twerppoet, I will add dropbox as well. Is this an app ?