You should be analyzing your parameters before you start your search to make life easier, e.g. like this:

use strict;
use warnings;

sub name_search {
  join '', map {$_->[0]} grep { 0<=index $_[0], $_->[1] and 0<=index $
+_[0], $_->[2] } @{$_[1]};
}

my @criteria;
my $letter = 65;
push @criteria, [ chr( $letter++ ), splice @ARGV, 0, 2 ] while @ARGV >
+= 2;

print name_search 'John Smith', \@criteria;
print "\n";
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Also, have a look at join. You could write, assuming you open your output file before the loop:

while(<$data>) {
  chomp;
  my @line = split /\t/;
  my $found_tag = name_search $line[0], \@criteria;
  print OUT1 join( "\t", $found_tag, @line[0..13] )."\n" if $found_tag
+;
}
close $data;
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