Same thing happened to me earlier this week with my other iPad. I was able to transfer 4022 books in about 55 minutes. I started off with 200 books and then kept increasing the number in each batch. After 2000 books I said the heck with this and successfully sent 2022 in one batch I used the wireless connection and the worst part for me was highlighting all those books at once. You do need to be patient once you hit send. I think the fact that I only sent ePub format and none had to be converted on the fly probably decreased the transfer time.
I have become obsessive about checking that auto update setting.
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