First, always make a NAND backup. I am not trying to put you down or anything, but the NAND backup is seriously the most important thing right now. And with sighax, it's gotten even better. So I can't stress enough to always make a NAND backup and if you don't have the space for one, buy a new SD card. An SD card is a lot cheaper than a 3DS. I am saying this because I actually care about wanting to help you and keep your system working.
Right, now where did the error happen? You mentioned after 90% of something? As well what guide were you using? Because the current 3ds.guide no longer requires safectrtransfer.