Japan has a lot of shops over the length and breadth of Honshu
Try the JMSA in the first instance who runs the Japan mini day and sells a range of products under the Valtain brand.
http://www.mini.j-msa.com/shops/I live near Hamamatsu in the center of Japan for part of the year so Dinky Garage is my first pick. It's an easy walk from the main station.
I have known Naoki Ishizuka for 20 years and he has been to Australia and the U.K. And speaks English well. He is a director of JMSA so he can point you to other shops in almost any location.
http://www.dinky.co.jpDinky classic is also in Hamamatsu and the owner Furuhashi deals in a mind blowing array of NOS mk1 parts. He runs the Annual Cooper Sunday Lunch. His shop requires a car to get to.
http://www.dinky-classic.com/main/main.htmlGarage J & B in Nagoya
Mini Muruyama in Tokyo
Turtle Trading in Yokohama
Garage Grace in Yokohama
Delta in Osaka
And another couple of hundred from there.