Variables that are sequentially or similarly named are almost always a sign that they belonged in a single data structure. For example, if you had placed the data into a hash of arrayrefs:

my %data;
$data{A} = [qw(a data goes here)];
$data{B} = [qw(b data here too)];
$data{C} = [qw(and here is c data)];
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Then the code to compare A to both B and C could have just been a loop changing an index or key value. This is especially true if you're about to introduce D, E, F as you say in your last paragraph.

For example, here's a quick way to invert the index, and figure out which elements each item is in (presuming simple keys):

my %seen_in;
for my $key (sort keys %data) {
  for my $value (values %{$data{$key}}) {
    $seen_in{$value} .= $key;
  }
}
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For "data", this will reveal "ABC". For "goes" this will be "A", and so on.