If I understand you correctly, you're after a pseudo-merge of the 3, row-aligned, arrays contained within @results - where ...

• $results[0] contains the DayOfWeek column
• $results[1] contains the ProductionLine column
• $results[2] contains the Output column
• Each of the above arrays is the same size.
• For each block in the ProductionLine array, the order of entries is always the same e.g. alphabetically ordered

If so, then maybe something along the following (untested) lines might suffice ...

use strict;
use warnings;

use Data::Dumper;

my @results;
while (<DATA>) {
        my @row = split;
        for (my $idx = 0; $idx < 3; $idx++) {
                push @{ $results[$idx] }, $row[$idx];
        }
}

# Assume @results already populated...
my ($day_of_week, $production_line, $output) = @results;
my @data_to_plot;

# Ignore the headers
for (my $idx = 0; $idx < 3; $idx++) { shift @{ $results[$idx] } }

###
# Extending an idea from [http://www.perl.com/doc/FAQs/FAQ/oldfaq-html
+/Q5.4.html]...
my %saw;
my %production_lines = ( map { $_ => [] } grep ! $saw{$_}++, @$product
+ion_line );
#
###

for (my $index = 0; $index < @$day_of_week; $index++) {
    push @{ $data_to_plot[0] }, $day_of_week->[$index] unless
        grep /^$day_of_week->[$index]$/, @{ $data_to_plot[0] };

    push @{ $production_lines{$production_line->[$index]} }, $output->
+[$index];
}

push @data_to_plot, ( map { $production_lines{$_} } sort keys %product
+ion_lines );

print Dumper \@data_to_plot;

__DATA__
DayOfWeek       ProductionLine  Output
2       CANNING 18353
2       MULTIPACK       14878
2       QUEST   911
3       CANNING 46775
3       MULTIPACK       42601
3       QUEST   1564
4       CANNING 81302
4       MULTIPACK       67542
4       QUEST   1879

.
.
[download]

results in...

!perl fred.pl
$VAR1 = [
          [
            '2',
            '3',
            '4'
          ],
          [
            '18353',
            '46775',
            '81302'
          ],
          [
            '14878',
            '42601',
            '67542'
          ],
          [
            '911',
            '1564',
            '1879'
          ]
        ];
[download]

Once more, sits back and awaits flames for bad code, style, karma etc...

Update:
Corrected typos
Tested - corrected 'features', added results

HTH ,