Here's my suggestion: wrap the expressions in subroutines, like this:

package Regs;
use strict;
require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = ();
our %EXPORT_TAGS = ( 'all' => [ qw(
 re1
 re2
) ] );
our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
our $VERSION = '0.10';

sub re1 {
  $_[0] =~ s/foo/bar/g;
}

sub re2 {
  $_[0] =~ s/xxx/yyy/g;
}
[download]

It's a bit ugly, but a Text::Template could generate it for you from a list of expressions extracted from your code.

Then you could use Devel::AutoProfiler on a modified version of your script, like this:

use strict;
use Devel::AutoProfiler;
use Regs qw(:all);

my $a = "fooxxxfoo";
my $b = "foo foo foo";

re1($a);
re2($a);
print "a is $a\n";

re1($b);
re2($b);
print "b is $b\n";
[download]

Devel::Autoprofiler will automatically generate profile wrappers (you should make sure Regs is the only module after it). Just run the program and it will generate a usage and timing report at the end of the output.