I understand now why you had 2 loops.
Try this, as before replace #test lines with your lines marked ##

#!perl
use strict;
use warnings;
my @test = (470,278); #test

my @Gkel=();
my @Gkel_gz=();
my @TT1=();
my @files = qw(
  Gkel_check.1.ABC.dat.gz
  check.1.ABC_TT1.dat
  check.1.AB_TT1.dat
); #test

##opendir( DIR, $dir );
##my @files = grep( /$pattern/, readdir(DIR) );
##closedir(DIR);
##chdir($dir);

# sort so that AB_ comes after ABC
foreach my $file (sort @files) {    
  # check gz file
  if ( ($file =~ m/^Gkel_/) && ($file =~ m/gz$/) ){   
    ## my $result = `gunzip -c $file|tail -1`;
    ## my $count = substr($result,22,8);
    my $count = 108418; #test  
    $Gkel_gz[0] = $file;
    $Gkel_gz[1] = $count; 
    # extract .dat file
    ## system(`gunzip -f $file`);
   } 
  
  # check TT1 files
  if ( $file =~ m/^check.*TT1.dat$/ ){
    ## my $result = `wc -l $file`;
    ## my ($count, $file_name) = split(' ',$result);
    my $count = shift @test; #test
    push @TT1,[$file,$count];
  }   
}

# process extracted file
##opendir( DIR, $dir );
##my @files = grep( /$pattern/, readdir(DIR) );
##closedir(DIR); 
##chdir($dir);
push @files,'Gkel_check.1.ABC.dat'; #test
foreach my $file (@files) { 
  # extracted file
  if ( ($file =~ m/^Gkel_/) && ($file !~ m/gz$/) ){   
    #my $result = `wc -l $file`;
    #my ($count, $file_name) = split(' ',$result);
    my $count = 107948;
    # remove Gkel from filename
    my $file1 = substr($file,5,50);
    $Gkel[0] = $file;
    $Gkel[1] = $count;
    #system(`mv $file $file1`);
  }
}

# Ouput
my @row1 = ('Jun-2013',    # 
$Gkel_gz[0],$Gkel_gz[1],   # zip filename and count
$TT1[0]->[0],$TT1[0]->[1], # ABC_TT filename and count
$Gkel[0],$Gkel[1]          # unzipped filename and count
);

my @row2 = (
$TT1[1]->[0],$TT1[1]->[1]  # AB_TT filename and count
);

print join ',',@row1,"\n";
print join ',',@row2,"\n";
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poj