Thanks for the 0.4 update, this mod feels essential to not miss out on anything.
Something you might want to consider adding to the instructions is the optional fourth step of deleting the now extracted images folder excluding "\classes\math101" (the only images your mod changes). This is to not unnecessarily double the game file size.
Also regarding UnRen option 9. I still use that choice cause I need some .rpyc decompiled for further modding (I remove the permanent changes to alignment after the major choices). You'll get plenty of errors from the decompiled rpy's, just delete the offending ones. Since the Ren'Py load order is (AFAIK): "compiled rpyc's -> uncompiled rpy's -> rpa's -> loose files", you can delete the later loaded ones and it defaults back to the earlier loaded (ie compiled versions).
I did these steps with both the 0.3.1 release and now this one, no issues so far. My modded version of 0.4 is 6,17 GB in 1634 files instead of 12,0 GB in 12000 files.
EDIT: The order I do it in is:
UnRen option 9 -> delete the images (and music) folder(s) - > unpack the mod -> run the game to generate an error log -> delete the offending rpy's -> run game again to verify it works, check that your mod still works -> apply my modifications.