The files from inside the "bin" folder should NOT be in the same folder as "zjs_repack.exe" and the two ISO files "ff12us.iso" and "ff12zj.iso". It is the "bin" folder itself (with all its original content inside) and the empty "temp" folder, that should be in the same folder as those three files when you start "zjs_repack.exe".
As for the ISO sizes it is apparent that these can vary considerably without much effect on the work of "zjs_repack.exe". My own "ff12us.iso" has yet a third size, of 3,969,856 KB.
Fortunately the program was made to cope with variations of ISO files, searching for stuff to patch relative to real content and never by absolute location.
Best regards: dlanor