Grub lives in none of the above. Grub lives in the MBR itself, Sector Zero. It loads stuff like grub.conf from another partition, but the MBR is the prime mover. Grub doesn't mount partitions since...
But are you certain that the partition you see is the boot partition? On some systems, like mine, /boot is a partition on it's own, not the root partition.
Hmm. cp or dd on a partition won't set a partition bootable, no, that's defined in the partition table, i.e. sector zero. Something like this will set Partition 1 bootable:
You don't need special commands, the ones you already have will work quite fine. Linux gives you special files for partitions that you can use the same way you use the special files it gives you for...