Oops, I was slightly wrong. Combinations will only replace three of your loops. You still have to select the applicable combinations.

use Algorithm::Combinatorics qw(combinations);

my $lep = int 1;
my $rep = int 100;
my $iter = combinations( [$lep+2 ..$rep], 3 );
while (my $c = $iter->next) {
    my ($x, $y, $z) = @$c;
    foreach my $s (1..$rep/4) {
        # as before
    }
}
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