I've not got a Touch, but what you are describing sounds like you are doing all the right things.
Make sure you are ejecting the Kindle from your PC when you are finished copying files (right click and select "Eject", or use "Safely Remove") like you would with a pen drive or external hard disk - don't just pull the cable out.
It's fairly normal for the home screen to appear after a restart with no books or categories in it, they all appear after a few seconds.
I'd be tempted to get onto Kindle CS (
http://www.kindleboards.com/index.php/topic,73465.msg1181468.html#msg1181468, use the "Call me back" option) and ask them to step you through the process.