This is working great with rxtools.
Was on Firmware V2 on old 3DS. Updated to 4.5 via Luigi's mansion rom via sky3ds kart
Installed gateway files and went to gateway app via browser exploit
Saved backup of system nand. Created emunand.
unlinked systemnand from emunand via formatting system with sd card removed and inserting later
Updated emunand to latest version 10.2
Installed RXtools 2.6 (Still some issues with mset and seems to do the installing on every entry - to look into it, but working
Installed FBI to emunand via rxtools
Installed some CIA game backups via FBI to emunand
Installed NTR CFW Cia file (with additional file in root) via FBI
placed some cheat plugins in root
Now can boot into rxtools via web browser exploit (via 4.5 system nand) and boot to emunand.
From there, NTR is run, and then the desired game rom and ingame cheats/screenshots work just fine

X and Y together brings up the ntr screen with some other options