Bootmii will not autoboot discs directly. I think savemiifrii can if you're on 3.2 or lower, but that relies on part of the system menu(or its IOS?) being there - which you deleted.
Plus, WSR only updates to v3.4. There are no games with even a 4.0 update AKAIK.
Did you complete the bootmii NAND backup and have a ~512MB nand.bin file? Did it complete the backup? Factory bad sectors are normal.