As promised, here's some skeleton code (and sample data) to get you started:

#!/usr/bin/perl

use strict;
use warnings;
use feature qw/say/;

my %data_hash = (
    "key0.1" => [
        {
            "key1.1" => 3.3,
            "key1.2" => 17.8,
            "key1.3" => -2.4,
        },
        {
            "key1.4" => 5.1,
            "key1.5" => 13,
        },
        {
            "key1.6" => -69,
            "key1.7" => 127,
            "key1.8" => 2.718,
            "key1.9" => 3.3,
        },
    ],
    "key0.2" => [
        {
            "key1.10" => 3.3,
            "key1.11" => 2.5,
        },
        {
            "key1.12" => -33,
        },
    ],
);

my %flat_hash = ();

foreach my $key0 (keys %data_hash) {
    foreach my $index (0 .. $#{$data_hash{$key0}}) {
        foreach my $key1 (keys %{$data_hash{$key0}->[$index]}) {
            my $new_key = "$key0-$index-$key1";

            $flat_hash{$new_key} = {
                "value" => $data_hash{$key0}->[$index]->{$key1},
                "key0"  => $key0,
                "index" => $index,
                "key1"  => $key1,
            };
        }
    }
}

foreach (sort { $flat_hash{$a}->{"value"} <=> $flat_hash{$b}->{"value"
+} } keys %flat_hash) {
    say $flat_hash{$_}->{"value"},
        ": key0 = ",  $flat_hash{$_}->{"key0"},
        ", index = ", $flat_hash{$_}->{"index"},
        ", key1 = ",  $flat_hash{$_}->{"key1"};
}
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I didn't integrate the %limit_hash part since it wasn't part of your question.

N.B. - you can probably do this more easily and naturally still using map, but I just came back from an Apple Family reunion and am not yet thinking in Perl again. ;)