I'm going to deal with just this section, I think once you understand/update what is happening here, everything else you have will work. 
my $id;   # ??
foreach my $window ( @{ $data{$id} } ) {

  # only pass windows with > min number of stats (i.e. >1 for now), an
+d
  # of course we also ignore any 'undef' windows.
  next unless scalar @{ $data{$id} }[$window] >= 2;

    foreach my $individual ( keys(%data) ) {

[download]
First, I think that you understand that having an undefined $id as a hash key won't work. And to fix this, you want to just rearrange your for loops. 
foreach my $id ( keys %data ){
  foreach my $window ( @{$data{$id}} ){

[download]

Just this will get you much further. There is still a problem with the second loop though, at least in how you use $window in the subsequent code. You are attempting to use $window as an index, but it's not an index. Since you have experience using Data::Printer, I suggest going ahead and checking out what $window is.

Now, the way to fix things with the fewest number of overall edits is to change the second for loop.

foreach my $id ( keys %data ){
  foreach my $window ( 0 .. $#{$data{$id}} ){
    next unless scalar @{ $data{$id}[$window] } >= 2;

[download]
Then in your method calls, just change those to align with the scalar test above: 
\@{ $data{$id}[$window] }

[download]
I hope that helps.

In reply to Re^2: Population of HoAoA based on file contents by state-o-dis-array
in thread Population of HoAoA based on file contents by iangibson

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