Like this? (Just a few minor tweaks :)

BTW, it was sorting, just not numerically.

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1198131

use strict;
use warnings;

my %one;

while(<DATA>)
  {
  my ($one, $two, $three, $four) = split;
  /(\d+)/; # get number for later sort
  push @{ $one{$1} }, [ $two, $three, $four, $_ ];
  }

for my $one (sort { $a <=> $b } keys %one)
  {
  my %groups;
LOOP:
  for ( sort {
    $a->[1] cmp $b->[1] or
    $b->[2] <=> $a->[2] or
    $a->[0] <=> $b->[0] }
    @{ $one{$one} } )
    {
    my ( $two, $three, $four, $all ) = @$_;

    if( keys %groups )
      {
      for ( sort keys %groups )
        {
        if( ( $_ ^ "$three" ) =~ tr/\0//c <= 2 )
          {
          push @{ $groups{$_} }, [ $two, $three, $four, $all ];
          next LOOP;
          }
        }
      push @{ $groups{$three} }, [ $two, $three, $four, $all ];
      }
    else
      {
      push @{ $groups{$three} }, [ $two, $three, $four, $all ];
      }
    }
  for ( sort keys %groups )
    {
    print "CLUSTER\n";
    print $_->[3] for values @{ $groups{$_} };
    }
  }

__DATA__
chrM:307    0    TCAGGGTG    115
chrM:307    0    TCAGGGTG    107
chrM:307    0    TCAGGGTG    115
chrM:307    0    TCAGGGTG    130
chrM:307    0    TCAGGGTG    114
chrM:307    1    TCAGGGTG    106
chrM:310    0    TCAGGGTG    99
chrM:392    2    CCTCTTAT    130
chrM:396    2    AGTTACTA    129
chrM:443    0    ATTATCAA    130 extra columns
chrM:542    2    AATCCAAA    129
chrM:542    0    AATCCAAA    129
chrM:934    0    CATTCGCT    129
chrM:934    1    CATTCGCT    129
chrM:1001    0    CGTGACAT    129
chrM:1127    0    GATACTAA    130
chrM:1257    1    TGGAAATC    129
chrM:1262    0    CGGGAAGC    129
chrM:1262    0    AGGGAAGG    129
chrM:1603    0    GTATCGGA    130
chrM:1603    1    GTATCGGA    130
[download]

Outputs:

CLUSTER
chrM:307    0    TCAGGGTG    130
chrM:307    0    TCAGGGTG    115
chrM:307    0    TCAGGGTG    115
chrM:307    0    TCAGGGTG    114
chrM:307    0    TCAGGGTG    107
chrM:307    1    TCAGGGTG    106
CLUSTER
chrM:310    0    TCAGGGTG    99
CLUSTER
chrM:392    2    CCTCTTAT    130
CLUSTER
chrM:396    2    AGTTACTA    129
CLUSTER
chrM:443    0    ATTATCAA    130 extra columns
CLUSTER
chrM:542    0    AATCCAAA    129
chrM:542    2    AATCCAAA    129
CLUSTER
chrM:934    0    CATTCGCT    129
chrM:934    1    CATTCGCT    129
CLUSTER
chrM:1001    0    CGTGACAT    129
CLUSTER
chrM:1127    0    GATACTAA    130
CLUSTER
chrM:1257    1    TGGAAATC    129
CLUSTER
chrM:1262    0    AGGGAAGG    129
chrM:1262    0    CGGGAAGC    129
CLUSTER
chrM:1603    0    GTATCGGA    130
chrM:1603    1    GTATCGGA    130
[download]