Word docs don't really have line numbers in the same way a text file does. Here is a search and replace sub that may point you in the correct direction. Another option is RTF format. It is easy to munge with Perl and REs but can retain most general formattion. YMMV.

sub word_find_and_replace {
    my ( $word, $rel_file_path, $tokens_ref ) = @_;
    # first make a temporary file to do the search and replace on
    my ( $fh, $temp_name ) = get_tempfile( "$DOC_DIR/system", 'doc' );
    close $fh;
    my $content_ref = read_file( "$DOC_DIR/$rel_file_path" ); 
    create_file( "$DOC_DIR/system/$temp_name", $content_ref, 'overwrit
+e ok' );
    $word->{visible} = 0;
    my $doc = $word->{Documents}->Open("$DOC_DIR/system/$temp_name");
    my $search_obj =  $doc->Content->Find;
    my $replace_obj = $search_obj->Replacement;
    for my $token ( keys %$tokens_ref ) {  
        my $find =  '<?' . $token . '?>'; 
        my $replace = $tokens_ref->{$token};
        # now i know this looks wierd but M$ word (at least 2000) want
+s \r
        # as the para marker not \r\n or even \n if you send \n you ge
+t little 
        # binary squares..... oh well that's M$ for you. 
        $replace =~ s/\r\n|\n/\r/g;  # this makes it work properly. GO
+K
        $search_obj->{Text}  = $find;
        $replace_obj->{Text} = $replace;
        $search_obj->Execute({Replace => $wdReplaceAll});
    }
    $doc->Save;
    $doc->Close;
    # now get the data out of the modified temp file
    $content_ref = read_file( "$DOC_DIR/system/$temp_name" );
    # remove our unwanted temp files and objects
    unlink "$DOC_DIR/system/$temp_name";
    undef $search_obj;
    undef $replace_obj;
    undef $doc;
  return $content_ref;
}
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