You've been most helpful! =)
So let's see if I've gotten this right:
I'll get a fresh card and start from scratch since I don't want copy the files on the second hand card that came with the 3DS to my computer because of the potential virus risk. Is it then necessary to also format my 3DS, and can I do so without losing Luma3DS? Other then boot.firm, do I need anything else on the SD card? I don't care for custom themes or homebrew atm, but I guess I need to get FBI (to play .cia-files) or will that still saved on the system memory?