The Japanese iPhone should be a GSM phone. You can check to see if you have a SIM tray on the right side of the device. If yes, it's a GSM, if no, it's a CDMA. If it's a GSM, use the iPhone3,1. If it's a CDMA, it's the iPhone3,3.
Depending on the iOS that's on your device currently, you'll need to use an IPSW that matches. iOS 6.0-6.1.3 requires the iOS 6.0 IPSW, regardless of whether it's 6.1, 6.1.2, etc etc. Otherwise, you'll need to use one that matches directly with the iOS on your device.
If you're on iOS 6.0 - 6.1.2 (6.1.3 not included) you can use Evasi0n instead of RedSn0w.
Unlocking a Japanese phone is probably one of the most expensive unlocks. Japanese carriers don't conventionally unlock devices, whether if you pay for it or not, this is where interposers shine.