I made a temporary script to fix the naming problem of the 3 eidolons. Put the "rename_eidolon.cmd" in "dmm" folder and run it after "3_write_config.py", the script will change the name of Apocalypse, Behemoth, Houou to correct one.
This fix is just temporary, I still need your "raw_scenario" folder to find the correct problem. If the size of the folder is a problem, you can delete the files that have "_script.json" and "_script.ks" to cut down the size. I also wrote a script for you to do this, just put "delete_script.cmd" in "raw_scenario" folder and run it, it should delete all "_script" file for you.