The only Perl-specific advice I can give is that two-dimentional array is quite bad datastructure for such purpose. If you need to process pairs of numbers, the best data structure is array of arrays containing these pairs, e.g.

@ary = (
  [1,2],
  [2,3],
  [3,3]
  #other data
)
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I wrote a simple code to solve your problem using this datastructure; it may be useful for you.

#!/usr/bin/perl

use warnings;
use strict;

my @ary= map { chomp; [split] } split /\n/, <<NUMS;  #sample input dat
+a
1 2
2 3
3 3
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 3
12 0
13 0
14 4
NUMS

my @result;
my @buffer;
my $xmax = $ARGV[0] || 4;  #get the xmax value from the command line
my $lasty;
foreach my $pair (@ary) {
    if ($pair->[1] != 0) {
        if (@buffer >= $xmax) {
            push @result, @buffer;
            @buffer = ();
        }
        if (@buffer && $lasty != $pair->[1]) {
            push @result, @buffer;
            @buffer = ();
        }
        if (@buffer && $lasty == $pair->[1]) {
            push @result, map { [$_->[0], $lasty] } @buffer;
            @buffer = ();
        }
        $lasty = $pair->[1];
        push @result, $pair;
        next;
    }
    push @buffer, $pair;
}

print join "\n", map { "@$_" } @result;
print "\n";
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