Here is how I would do it. Note I'd class this as fairly advanced perl - hash refs, array refs all nested etc, but an idiom well worth picking up.

#!/usr/bin/perl -w

use strict;
my ($key);

# Collect the data
my $data = {};
while (<>)
{
    chomp;
    my @row = split /,/;
    next unless @row;
    $key = shift @row;
    # the following is the most important line in the program
    # understand it and you've got it!
    push @{$data->{$key}}, [ @row ];
}

# Uncomment these lines if you have Data::Dumper and you want to see
# what the data structure looks like
# use Data::Dumper;
# $Data::Dumper::Terse = 1;
# print Dumper($data);

print "Total count\n";
for $key (sort keys %$data)
{
    print "  $key has ", scalar @{$data->{$key}} , " entries\n";
}

print "Second and third items of all QTYs\n";

for $key (@{$data->{QTY}})
{
    print "  $key->[0], $key->[1]\n";
}

print "Third items in HDRs\n";

for $key (@{$data->{HDR}})
{
    print "  $key->[1]\n";
}

print "4th and 5th items in OTIs\n";

for $key (@{$data->{OTI}})
{
    print "  $key->[2], $key->[3]\n";
}
[download]

Run this with

  perl progname.pl 824.txt

When I run it on your test data it produces this output

Total count
  AMT has 3 entries
  BGN has 1 entries
  HDR has 1 entries
  OTI has 2 entries
  QTY has 4 entries
  TED has 2 entries
Second and third items of all QTYs
  46, 10
  53, 0
  54, 10
  55, 0
Third items in HDRs
  200008081441EST
4th and 5th items in OTIs
  WEDI620000802, 159
  0021000095, 159