you have an error at:

  my @new = split //, $new;
  my $longer = (@cold > @new) ? $#cold : $#new;
[download]

Which should be:

  my @cnew = split //, $new;
  my $longer = (@cold > @cnew) ? $#cold : $#cnew;
[download]

And at:

  substr ($old, subscr, 0) = $span;
  substr ($new, subscr, 0) = $span;
[download]

Which should be:

  substr ($old, $subscr, 0) = $span;
  substr ($new, $subscr, 0) = $span;
[download]

Also this:

  my $losubscr; #two subscripts because differ len of new and old
  my $lnsubscr; 
  @cold = reverse @cold;
  @cnew = reverse @cnew; #we're gonna search these backwards
  for (0..$longer) { 
    if ($cold[$_] ne $cnew[$_]) {
        $losubscr = @cold - $_;
        $lnsubscr = @cnew - $_;
        last;
    }
  }
  #got pertinent subscripts, now insert span tags
  substr ($old, $losubscr, 0) = $espan; 
  substr ($new, $lnsubscr, 0) = $espan;
  substr ($old, subscr, 0) = $span;
  substr ($new, subscr, 0) = $span;
[download]

Could be shortened to:

  my $lsubscr;
  @cold = reverse @cold;
  @cnew = reverse @cnew; #we're gonna search these backwards
  for (0..$longer) { 
    if ($cold[$_] ne $cnew[$_]) {
        $lsubscr = -$_;
        last;
    }
  }
  #got pertinent subscripts, now insert span tags
  substr $old, $lsubscr, 0, $espan;
  substr $new, $lsubscr, 0, $espan;
  substr $old, $subscr, 0, $span;
  substr $new, $subscr, 0, $span;
[download]

Another way to write that would be:

while ( defined( my $first = <DATA> ) && defined( my $second = <DATA> 
+) ) {
    print spandiffstr( $first, $second );
    }

sub spandiffstr {
    my ( $old, $new ) = @_;
    my $span = '<span>';
    my $espan = '</span>';
    ( $old ^ $new ) =~ /^\0*/ and my $subscr = $+[0];
    my ( $rold, $rnew ) = map scalar reverse, $old, $new;
    ( $rold ^ $rnew ) =~ /^\0*/ and my $lsubscr = -$+[0];
    # got pertinent subscripts, now insert span tags
    substr $old, $lsubscr, 0, $espan;
    substr $new, $lsubscr, 0, $espan;
    substr $old, $subscr, 0, $span;
    substr $new, $subscr, 0, $span;
    return $old, $new;
    }
[download]

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