I have the same problem! It's weird that most people were able to update their R4i Gold 3DSes without any issues and just a few people are having this problem. I emailed r4ids.cn about it and they already replied saying they're trying to figure it out. They seem like a pretty good team to me...
I've been playing fallout4 all day, I went into a elevator and it kept going, never stopped, waited 5 minutes, must of been a bug. How bout you, whatcha do today?