Hi,
1. Another email is not possible easily (unless you develop a whole plugin, and in that case, supposing you're a developer, you can use the onAfterOrderUpdate trigger in your plugin to do your own code after an order's status is changed to "confirmed" and send the email).
I would recommend to simply edit the email in the menu System>Emails and customize the area where the link is added in order to make it more obvious. There, you'll find the tag {LINEVAR:PRODUCT_DOWNLOAD} you can add some extra HTML tags around it with some CSS to make it bigger, bold, etc.
2. Yeah, either you upload each file in the same "ebook" variant, or you actually create an extra variant so that you get three choices (paper, epub or pdf) instead of two (paper and ebook).