I wrote something up, but Zaxo (and now rir) beat me to the punch, so instead here's some code to convert your arrays into a single hash:

my %gene = ();
foreach (@gene_score) {
  $gene{$_->[0]}->{score} = $_->[1];
}

foreach (@gssc) {
  $gene{$_->[0]}->{start} = $_->[1];
  $gene{$_->[0]}->{stop} = $_->[2];
  $gene{$_->[0]}->{chr} = $_->[3];
}
[download]

Now %gene looks like:

%gene = ( gene_name_0 => { score => 'score_0',
                           start => 'start_0',
                           stop  => 'stop_0',
                           chr   => 'chr_0' },
          gene_name_1 => { score => 'score_1',
          ...
        );
[download]

Brad