Is there any way of doing a clean install on an Amazon EC2 instance. I have the bootable installation media stored in an EBS volume. How can I boot from that volume? And do I have to use an automated install (install script) then, since I won't be able to oversee the boot procedure and all the settings that need attention during the installation process.
You will not be able to do this. EC2 does not support booting from anything but AMI images.
You'll need to wait until they release an official 2012 image.