If you still can't get the file-sharing to work, there is a way to send books directly to your Kindle app on the iPad. You'll have to install an
Amazon program called "Send to Kindle for PC" (details here:
http://www.amazon.com/gp/help/customer/display.html/?nodeId=200768410), but once it's installed, you can send anything the Kindle app can read to your iPad app.
It's pretty cool, cause you don't have to have an e-mail client or iTunes open on your PC (or the iPad connected to the PC). You can just send it using
Amazon's servers. And, if you choose, you can have
Amazon keep the file/e-book in your Personal Documents in their cloud so you can sync across devices or just store the e-book on
Amazon's servers.
You probably can tell I like this service.
But, it is a valid option if you can't get yours working properly.
Marilyn