so i've changed the in the save files but saves not changed. what should i do next
Not sure what you're trying to say, but you should extract Koga's mod to the game's "Game" folder and overwrite. Not the saves folder! See the included info and always make sure you're using the same versions of the game and mod.
As a rule of thumb, when I use a mod, I
always use the same mod afterwards. Otherwise things might get broken if the mod adds it's own variables to the saves. I can't tell you if it's OK to start using the mod halfway through the game, as my knowledge is very limited, but I think it would be OK. But you can always start fresh and skip to choices.
Or better yet, take the chance to replay some memorable scenes... and there are a lot!