You probably want to use a nested hash...

In the first set of loops, where you have:

$ID = $Fields[6];
push (@id, $ID);
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change it to:

$ID = $Fields[6];
$id{$ID}{count}++;  # keep track of unique ID counts
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[Don't forget to declare my %id with your other variables. And use warnings; and use strict;]

Then later you have:

foreach $id(@id)
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rework this for the hash as:

foreach my $id(keys %id)
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When you find the transport, add it to the hash like this:

$id{$id}{transport} = $TRANSPORT;
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You can print this out right here if you like:

printf "%-20s %5d %10s\n", $id, $id{$id}{count}, $id{$id}{transport};
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[though you will want %-5d if you really need the numbers left justified in the field.]

Update: I don't know how you keep track of IDs in the transport section. There seems to be a typo at $Clec_id.

Also, the transport section is not efficient. You can probably construct it similar to this:

foreach $FTP_Lines(@FTP_Lines)
{
  chomp $FTP_Lines;
  @FTP_fields = split (/\;/, $FTP_Lines);
  if ( defined($id{$FTP_fields[0]} )
  {
    $TRANSPORT = $FTP_fields[7];
    $id{$id}{transport} = $TRANSPORT;
    printf "%-20s %5d %10s\n", $id, $id{$id}{count},
                               $id{$id}{transport};
  }
}
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-QM
--
Quantum Mechanics: The dreams stuff is made of