Eshop code from Amazon Japan is quite cheap compared to buying locally.
I think the process for this would be moving my account over to Japan, which would also move his, redeeming the eshop code on his account , then switching region back to our local one.
Have I understood that correctly?
No idea about that, but same rules apply, so if you both have 0 balance, try changing and the account and see. Worse case scenario you will have to change region for two accounts instead of one.