You could simplify your code a lot by working with hashes instead of arrays.

use List::Util 'sum';

while (<TABFILE>) {
   my @fields = split /\t/;
   my $identifier = shift @fields;

   my ($category, $group) = ($identifier =~ /^TS(\d+)(\w+)/);
   warn "Parse error", return unless $category && $group;

   # This may not be what you're doing, but change 
   # this to do the calculations you need to do
   $sums{$group}->{$category} += sum(@fields);
   $totals{$group}->{$category} += @fields;
}

# Another way of cleaning up bad data
foreach (keys %sums) {
   $sums{$_}->{CCFN30NT} += delete $sums{$_}->{CCCFN30NT};
   $totals{$_}->{CCFN30NT} += delete $totals{$_}->{CCCFN30NT};
   ...
}
[download]

Also note that Excel can work with CSV or tab-delimited files natively, and more importantly, you can use formulas in Excel to calculate a lot of this. Your script need only output an Excel formula in a field (preceded with an equal sign) instead of calculating the value in advance.

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