Okay this will work, for 3 weeks I tried to get this to work and finally did it. I also understand why you want to do it and the end game: you want a donor Japanese console to do system transfer to from Japanese 3ds, then do region change and have full eShop access.
So i had many broken new 3ds parts. I stitched a Frankenstein new 3ds enough to boot with USA motherboard. First i did a system transfer from the Frankenstein new 3ds to a random new USA 3ds i had. Once completed, i did a region change to Frankenstein 3ds and change to Japanese. Ta-da eShop work and it was now 100% japanese region, right?
No matter, how many times i attempted to do a system transfer to this Frankenstein new 3ds, it always failed on step 5/5 eShop with code 005-5414. This Frankenstein had full japanese eShop, so was so confused. Solution: go to eShop > settings (bag/last option)> delete (2nd to last option) > you will be ask to confirmed and to enter system serial number. Afterwards, system turns off, access eShop again and set up.
Now all system transfer will complete
i think you will have to repeat this eShop deletion account every time, even though system has not eShop account register, something gets logged or recorded in Nintendo servers, and deleting it allow system transfer to work.
This only applies to this unique scenario and vision we both had and discovered. Enjoy.