I did a little research to see if there was anyone who had tried to clone the way I had mentioned in the first post, and it turns out you can't do it without backing up the NAND data on the 3DS itself as well as the SD card.
The NAND data is apparently stored on an SD card like thing on the bottom of the 3DS which requires soldering to get to which will void my warranty if I try it.
The only option I have now is to clone the same way as everyone else (the trade and turn off method) however, I've tried turning my 3ds off in mid-game by using the power button, but my 3DS doesn't always turn off at the exact moment that I press it.
Is it possible to shut the game off prematurely by taking the SD card out in mid-trade?
I've taken my SD card out of my 3DS while it has been turned on before and it makes a black screen message pop up as a result which turns off any game I'm playing at the time. I'm wondering if I can clone by doing it that way rather than turning it off.
I don't actually know the full details on how to clone via the trade and turn off method, could someone give me instructions on how to do it?