Oh, in that case you don't need to copy into the Data/Mods/%Modified Main%/ folder at all. Just having the Public files merged together like that is all that's necessary.
Oh right, So I don't need to copy anything into Data/Mods/%Modified main%. That is where I was going wrong then, I thought I needed to copy the files from data/mod of each mod I am using into Data/Mods/%Modified the same as copying the ones from public.
