Maybe you want to look at Regexp::Common::balanced. Using it I get this: Updated and cleaned up in response to anirbanphy's post which follows:

use Data::Dumper;
use Regexp::Common;
use strict;
use warnings;

my $pin_group_re=qr{
        pin\ +                                  # "pin" followed by sp
+aces
        (                                       # $1 capture
            $RE{balanced}{-parens=>'()'}        # balanced parenthesis
            \ +                                 # followed by spaces
            $RE{balanced}{-parens=>'{}'}        # balanced braces
        )                                       # end $1 capture
        }x;
my $timing_group_re=qr{
        timing\ +                               # "timing" followed by
+ spaces
        (                                       # $1 capture
            $RE{balanced}{-parens=>'()'}        # balanced parenthesis
            \ +                                 # followed by spaces
            $RE{balanced}{-parens=>'{}'}        # balanced braces
        )                                       # end $1 capture
        }x;

    sub do_something_with_a_pin {
        # To see what we got we'll dump @_
        warn Data::Dumper->Dump([\@_],[qw(*_)]),' ';
        my $string=shift;

        if ($string =~ m{direction : input}) { # Has a "direction : in
+put" so no modification
            warn "has 'direction : input'";
            }
        elsif ($string =~ m{$timing_group_re}) { # has a timing group
            warn "has 'timing'";
            # kill the max_transition line --
            $string =~ s{^.*max_transition.*\r?\n}{}m;
            # Let's see what the string looks like now
            };
        warn Data::Dumper->Dump([\$string],[qw(*string)]),' ';
        return $string;
        };

my $string;
{
    # Because we want all of the data as a single string
    local $/;
    # Deal with string, which will be the entire file, replacing each 
+of pin groups
    ($string=<DATA>) =~ s{$pin_group_re}{"pin\ ".do_something_with_a_p
+in($1)}gex;
    }
print $string;

__DATA__
IN_FILE
  cell (lib_1) {
    dont_use : true ;
    dont_touch : true ;

    pin ("HIZIBI_IN_1") {
      direction : input ;
      clock : true ;
      max_transition : 1 ;
      capacitance : 12 ;
    }
    pin ("HIZIBI_79")    {
      direction : output ;
      max_transition : 10;
      min_capacitance : 3 ;
    }
    pin ("HIZIBI_IN_1") {
      direction : input ;
      clock : true ;
      max_transition : 1 ;
      capacitance : 1 ;
    }
    pin ("HIZIBI_78")    {
      direction : output ;
      max_transition : 10;
      min_capacitance : 34 ;
      capacitance : 34 ;
    }
    pin ("HIZIBI")    {
      direction : output ;
      clock : true ;
      max_transition : 20;
      related_power_pin : VDD ;
      related_ground_pin : VSS ;
      timing () {
        cell_fall (into_f1) {
          index_1("1,2,3,4,5") ;
          index_2("1,2,3,4,5") ;
          values("13, 13, 14, 16, 18",\
                 "13, 14, 15, 16, 19",\
                 "14, 15, 16, 17, 20",\
                 "15, 15, 16, 18, 20",\
                 "15, 16, 17, 18, 21") ;
        }
      }
    }
  }
[download]

Now the last pin group looks like

   pin ("HIZIBI")    {
     direction : output ;
     clock : true ;
     related_power_pin : VDD ;
     related_ground_pin : VSS ;
     timing () {
       cell_fall (into_f1) {
         index_1("1,2,3,4,5") ;
         index_2("1,2,3,4,5") ;
         values("13, 13, 14, 16, 18",\
                "13, 14, 15, 16, 19",\
                "14, 15, 16, 17, 20",\
                "15, 15, 16, 18, 20",\
                "15, 16, 17, 18, 21") ;
       }
     }
[download]

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