print $fh substr($fc, $start, $numbers[$i]) ;

The @numbers array seems to be a sequence of start positions (offsets), but substr has the syntax
    substr EXPR,OFFSET,LENGTH
so perhaps
    print $fh substr($fc, $start, $numbers[$i]) ;
needs to be (untested)
    print $fh substr($fc, $start, $numbers[$i] - $start) ;
in the posted loop code.

(This assumes you've got your file read-writes properly binmode-ed now.)

Update: Minor changes (update: and a link added) for clarity.