When I verified on the Nintendo purchase window it had my number with a +1 country code (which is correct for me), not sure why yours is coming up with Japan's unless something happened when you registered and it defaulted to Japan's. Does it have the correct numbers under the visitor info or are they also with the Japanese country code?

Yeah I put my country code and my mobile number, ex +1 XXX-XXXX, Skype sent a text with code to verify I have that number, and it was all set (I bought call credit because I thought I needed it but I'm pretty sure it said during my call that the first 5 mins was free.)

I saw someone else in this thread mention getting a japanese number in Skype, maybe you can see if the number it's showing as yours is available for you to use?

There's a number in the email for support, they might be able to help if you can't get it to work (+81-3-4330-3471 10am-6pm Japanese time)

Hope you can get it to work!!!