This is a bit old, but I think I have a solution. If you're using a Japanese 3DS thats been language swapped, install FBI if you somehow haven't, go into titles, and find Nintendo Network ID Settings (it'll be below any of your installed games). From there, make/log into an NNID that's not being used on another 3DS, and it'll link. This'll allow you to use things like rverse (a miiverse revival app) and other system apps, but I'm not sure if it'll still need the eShop to actually boot into the game. I don't think it will tho.
Edit: Works like a charm, just took a little time to download the rest of the needed files.