romfs and exefs is something you unpack and extract from the 3ds/cia.
Thus, this goes back to what he said about:
You could try this tool, though I personally don't use it, so if you encounter any issues, I won't be able to help you with it. In any case, this thread is meant for issues relating to the functionality of pk3DS, so make sure any further posts you have on this thread is about that.