As always there is more than one way to do it. I see chains as arrays, so i built arrays first, then looped those to make hashes. Of coures as I wrote this and pasted I realized that this method depends on the right order, so I'm gonna make a second shot, but here is this version for fun:

#!/usr/bin/perl
use strict;
use warnings;

use Data::Dumper;

my $pairs = {
    (4,-1),
    (2,6),
    (6,4),
    (3,5),
    (5,-1),
    (99,-1),
};


my @paths;

foreach my $key (keys %$pairs) {
    my $value = $pairs->{$key};

    # if the right hand side matches the start of a chain
    # then unshift the left onto the start of the chain
    my @start_path = grep { @$_[0] eq $value } @paths;
    unshift(@{$start_path[0]}, $key) if @start_path;

    # if the left hand side matches the end of a chain,
    # then push the left hand side onto the end
    my @end_path = grep { @$_[-1] eq $key } @paths;
    push( @{$end_path[0]}, $value) if @end_path;

    push @paths, [$key, $value] unless (@start_path or @end_path);
}

my $hh;
for my $path (@paths) {
    my $temp = pop @$path;
    my $key  = shift @$path;
    for (reverse @$path) {
        my $t = {$_ => $temp};
        $temp = $t;
    }
    $hh->{$key} = $temp;
}
print Dumper($hh);
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