You could try a less ambitious filter that timed lines containing an "=~", something like this:

package Filt;
use Filter::Simple;

FILTER {
   my @set = split /\n/,$_;
   my $new = '';
   foreach my $line (@set) {
      if ($line =~ /\=\~/) {
         $new .= "\$t->start('$line');\n";
         $new .= $line . "\n";
         $new .= "\$t->stop();\n";
      } else {
         $new .= $line . "\n";
      }
   }
   $_ = $new;
};

1 ;
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I tried it on the following simple case, and it worked.

use strict;
use Benchmark::Timer;
use Filt;

our $t = Benchmark::Timer->new();
my $short_line_threshold = 2;
my $short_line_counter = 1;
my $long_line_threshold = 7;
my $tmp = "Abcdef";
$tmp =~ s/((?:<line>\s*(?:.{1,$short_line_threshold})<\/line>\s*){$sho
+rt_line_counter,})(<line>\s*(?:.{$long_line_threshold,}?)<\/line>)/$1
+<\/para><para>$2/gs;

print $t->report();
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