You can sync them with iTunes and sync them to iBooks. The article below will assist with setting up that sync.
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Thanks Norm! That got them onto my iPad! Now Im having an issue that I cant access any of them because I think there is too many? It is extremely slow and mostly stuck on the home screen. Was able to open one pdf but couldnt scrub through pages. Also cant browse through the pdf library. I thought maybe its like this because it needs to generate previews for all 4000 pdf's but its been over an hour now and still seems to be thinking. Tried to restart iBooks with the same result.
Would an ipad app such as PDF Reader Pro Edition for ipad help? Many reviews indicate that it works well with long textbooks, and long pdfs. It also lets you annotate, etc. You can also store your pdfs within the app.
It's $9.99 in tha app stores. Read the user reviews to learn more and see if it might help your issue.
Hope this helps.
I'm happy your problem was solved. And now many of us know when uploading many pdfs to ipad we need to be very patient!
I still think if you need to do more with your pdfs (annotate, organize, sign with your signature) you might consider PDF Pro edition for ipad or one of the many, many, other pdf apps out there. (I think I also might prefer PDF Expert - still checking them out. My husband brings home large files of info to read and the files often sit too long before he can get to them. I now scan them into pdf files and send them to his ipad (then shread the hard copies.) With one of these apps on his ipad, it will be easier for him to take notes, etc. - which is why he liked keeping the hard copies.)
Again, happy that you're up and going. Enjoy!