You have to write the boot tracks. If you read my post about installing OS X, the steps are buried in there. You will need the Install Pack download, the folder V2, and then you'll need to run the pre-patch script. That script writes the boot tracks.

In terminal, you do this:

sudo -s
cd /V2
./pre-patch.sh

This assumes you've put V2 in your root directory. After that, the clone should be bootable. BTW, the drive has to be a GUID partition to be bootable. If you didn't partition it that way, you'll have to go back and start over.