I'll make the same assumptions as the OP.
You have a working NAS with an optical drive and a console.
1. Boot a live CD with gparted. I used the live CD iso from gparted.
2. Copy the boot partition (16Mb) from your current boot device to unallocated space on your first hard disk and flag as bootable.
Note the partition. In my case it was /dev/sda4 If yours is different, adjust the next steps accordingly.
3. Remove the live CD and boot from your current boot device.
4. At the GRUB boot screen, press 'c' and enter the following:
grub> root (hd0,3)
grub> setup (hd0)
grub> {Esc}
5. Resume booting from your current boot device.
6. Login as root. With DSM5 beta I can do this at the console. With 4.3 I use PuTTY.
7. Type fdisk -l to verify your new boot partition.
8. Mount the partition and edit grub.conf as follows:
DiskStation> mount /dev/sda4 /mnt
DiskStation> vi /mnt/boot/grub/grub.conf
change 'root (hd0,0)' to 'root hd(0,3)'
9. Poweroff, remove your current boot device, and boot from the hard disk.