I know there is a post like this one with a solution, however, I have the same issue and it's persisting. What happened was, basically, I performed a system transfer from my main n3ds to a donor n3ds to region change my system to get it to be able to properly use the eshop and such. I messed up and ended up setting the system up anyway in JP before using cfw to region change to US. So I saw that the eshop still didn't work and used the default CTR NAND image from the 3ds.hacks site to restore my region. When doing a system transfer with my system, it now just throws the 005-5999 error.
TL;DR - same issue as solved question on GBAtemp but I don't have the original NAND backup as I overwrote it with the US region almost instantly.
TL;DR - same issue as solved question on GBAtemp but I don't have the original NAND backup as I overwrote it with the US region almost instantly.