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"Kernel Panic: NO init found message
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What kernel is lying in the partition? which distro it seeks to run? are you using an initrd.gz ? What boot loader are you using and how is it configured?
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I recall it asking if I wanted to transfer the MBR to make the cloned drive bootable. I saw nothing like that this time.
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Probably because, as you stated, you were backing up partition by partition, not the entire hard drive. The MBR is not contained in the partition but at the head of the hard disk to contain the general map of partitions.
If you have saved a copy of the original MBR it is good to restore that. However, if none, still you can manage to repair the MBR there are linux repair CDs that can read the geometry of the hard drive and write the map into the MBR, try one,
download from here burn and use.
Good luck.