Alright, final stretch! Here's what to do now:
# Remove the 010101 backup file from /gm9/out/ . Store it somewhere safe.
# Download GodMode9 from [link|https://github.com/d0k3/GodMode9/releases|here.]
# Copy GodMode9.firm to the root of your SD card and rename it to boot.firm
# Copy the /gm9/ folder to the root of your SD card. Overwrite files if it asks.
# Eject the SD card and reinsert it into your 3DS
# Insert the flashcart and boot from it (START + SELECT + X + magnet)
# If done correctly, you will have booted into GodMode9
# Press HOME, then select Scripts... > GM9Megascript > Restore Options > SysNAND Restore (full)
# Select your NAND backup
# Press A to unlock SysNAND (lvl3) writing, then input the keycombo given
# When the script finishes, press A to continue
# Press B to return to the main menu, then select Exit. Relock write permissions if it asks
# Hold R and press START to poweroff
# Insert your SD card back into your computer
# Download Luma3DS from [link|https://github.com/LumaTeam/Luma3DS/releases/latest|here.]
# Copy boot.firm and boot.3dsx to the root of your SD, overwriting the existing boot.firm
# Eject the SD card and reinsert it into your 3DS
Then just power on and hope for the best.