Don't bother with any region changer, if you just want to run the discs use DML. Use a loader to enable the Japanese patch.
For formatting the card just let the game do it.
As a recommandation get a cheap 4GB SD card or flash drive, and use clean rip to dump the games, then use devolution to load them. Devo has the most features and compatibility, and you can setup individual memory cards so Jpn games don't require any user input. You can even use the wiimote to exit, reset, etc.