This one (AutoCIA) for me converts the most ROMS (While still having a GUI to help me.) :
http://www.elotrolado.net/hilo_hilo-oficial-autocia-tutorial-3ds-a-cia-y-mucho-mas_2053343
But since that one doesn't have a tutorial, use this tutorial instead :
https://gbatemp.net/threads/tutorial-converting-3ds-to-cia-for-dummies.373722/
What I'm doing is a hybrid of the two.
-Use the files in the tutorial to create ncchinfo.bin
-Then copy the xorpads and the 3DS ROM to AutoCIA to convert them to CIA.
http://www.elotrolado.net/hilo_hilo-oficial-autocia-tutorial-3ds-a-cia-y-mucho-mas_2053343
But since that one doesn't have a tutorial, use this tutorial instead :
https://gbatemp.net/threads/tutorial-converting-3ds-to-cia-for-dummies.373722/
What I'm doing is a hybrid of the two.
-Use the files in the tutorial to create ncchinfo.bin
-Then copy the xorpads and the 3DS ROM to AutoCIA to convert them to CIA.