So I started in the War of Conquest scenario as Aegon the Conquerer, and I never converted to the Faith of the Seven, instead choosing to remain Valyrian... and yet, the High Septon still exists. How do I abolish the organized religion of the Faith of the Seven and replace it with Valyrian? It seems like that is a much needed feature. I would suggest scripting this into the event where you choose to convert or remain Valyrian religion after conquering the Reach as Aegon... If you choose to remain Valyrian, you should burn the Starry Sept at Oldtown to the ground with your dragons and establish a new organized Valyrian religion... or something similar.
Also, the mod itself is very Faith-of-the-Seven-centric. Even for characters who are not Faith of the Seven (like my Valyrian Targaryen dynasty), the event text in the game mentions 'septons' and 'septas' quite a lot. I assume that with the new religious diversity of Essos in the upcoming additions, this will be fixed and the mod will no longer seem as if it's only meant to be played with Faith of the Seven characters.