PEBCAK. By that I mean you've done something you shouldn't have.
Disable all other mods.
Don't put any mods into the folder that has the "DontPutModsHere.txt" file (which is located in the Steam CK2 folder). https://ck2.paradoxwikis.com/Mods#Installation
Don't interrupt the download once it's going.
Use the included .mod file, do not create your own.
I had some trouble setting up the SVN program after i installed it and i think that might have messed up the download of the mod. I deleted Tortoise and the EKSVN folder and then reinstalled both. I just started up the game and the cultures/ religions are showing up as they should so i hopefully its fixed.