use strict;
my @array = qw/ ***1*** first second ***end1*** ***2*** third fourth ***end2*** /;

my @new_array;
foreach my $element ( @array ) {
    my $mark = quotemeta "***";
    my $where = ( $element =~ /$mark(\d+)$mark/ .. $element =~ /${mark}end$1+$mark/ );
    push @{$new_array[ $1 - 1 ]}, $element if $where != 1 and $where !~ /E/ ;
}

use Data::Dumper;
print Dumper \@new_array;