my $EngWales_First_cat_observed;
  my $EngWales_First_cat_DSRs;
  my $EngWales_First_cat_Lower_95_Confidence_Limits;
  my $EngWales_First_cat_Upper_95_Confidence_Limits;
  
  my $EngWales_Second_cat_observed;
  my $EngWales_Second_cat_DSRs;
  my $EngWales_Second_cat_Lower_95_Confidence_Limits;
  my $EngWales_Second_cat_Upper_95_Confidence_Limits;
  
  my $EngWales_Third_cat_observed;
  my $EngWales_Third_cat_DSRs;
  my $EngWales_Third_cat_Lower_95_Confidence_Limits;
  my $EngWales_Third_cat_Upper_95_Confidence_Limits;

  my $PlaceX_First_cat_observed;
  my $PlaceX_First_cat_DSRs;
  my $PlaceX_First_cat_Lower_95_Confidence_Limits;
  my $PlaceX_First_cat_Upper_95_Confidence_Limits;
  
  my $PlaceX_Second_cat_observed;
  my $PlaceX_Second_cat_DSRs;
  my $PlaceX_Second_cat_Lower_95_Confidence_Limits;
  my $PlaceX_Second_cat_Upper_95_Confidence_Limits;

  my $PlaceX_Third_cat_observed;
  my $PlaceX_Third_cat_DSRs;
  my $PlaceX_Third_cat_Lower_95_Confidence_Limits;
  my $PlaceX_Third_cat_Upper_95_Confidence_Limits;

  my $Sex_specificity;
  
  my $Comparitor_file_statistic;
  my $Comparitor_file_age_group;
  my $Comparitor_file_period;
  my $Comparitor_file_scale;
[download]

the "first", "second", "third" in the code above is probably better expressed using arrays where the numbers 0, 1, and 2 give you the first, second, or third element.

overall, I think this program could benefit from an understanding of data structures, particular array and hash references. "Advanced Perl Programming" 2nd edition was great for this. 3rd edition by Cozens is a completely different animals. So, I recommend that you read perldsc and think hard about how it's contents could improve your program.

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