I've fixed this problem thanks to the the Story17 image archive guide in post #579. You might have to manually edit the config.ini file after running 3_write_config, I had to at least. I've included a screenshot of the config entries and the file itself in the GIF archive.
Edit 1: Some of the audio files weren't downloaded by the Nutaku 1_download_assets, so I copied the ones from my DMM player into the Nutaku assets folders, then ran 2_build_rpy so the scenes would have all of the audio.
Edit 2: I don't fully understand the interaction between the harem_main_quests file, 3_write_config, and config.ini. The main issue seems to be that 3_write_config changes 'name = story_18' to 'name = 18' under the '[story_18]' entry. I had a similar problem, described in post #626, and it was solved by post #630. The current options are to tinker with the files until Main Quest 18 works like the other MQs, or wait for a programmer fix it and keep editing config.ini until then. As the the Nutaku MQ intro audio, I don't know how to fix 1_download_assets but I could upload the files onto pixeldrain. I'll post a link when it's ready.
Edit 3: Nutaku Kamihime Player Main Quests 1-18 Intro Scene Audio, run 2_build_rpy after placing the folders in the 'assets' folder.