Your solution is not very efficient because it iterates too much unnecessarily. What you need is to build a hash table to store the necessary data before printing them at the end. Here's my attempt at your code...

#!/usr/bin/perl
use strict;
use Getopt::Long;
use Data::Dumper;
use IO::File;

&GetOptions( 'd|date=s' => \(my $DATE),
             'p|path=s' => \(my $PATH),
             'h|help'   => \(my $HELP) );

usage() if defined $HELP or ! (defined $DATE || defined $PATH);

$PATH = "/Ack/$DATE" unless defined $PATH;
my $ftpoutbound = "/homes/ftpoutbound.db";

my @FileList;
opendir (DIR, $PATH) or die "Can't open dir $PATH $!";
while (my $f = readdir(DIR))
{
    next if -d $f;
    push @FileList, $f;
}
closedir DIR;

# print Dumper(\@FileList);

my %data;
foreach my $file (@FileList)
{
    my $f = new IO::File "$PATH/$file", "r"
                or die ("can't open $PATH/$file :$!");
    while (<$f>) {
        my @rec = split /[\|\*~]/;
        if ($rec[5] eq "ZZ") {
           my $id = $rec[6];
           $id =~ s/\s+//;
           $data{$id}{COUNT}++;
        }
    }
}

# print Dumper(\%data);

# merge data into %data structure with values from FTP file
my $f = new IO::File "$ftpoutbound", "r"
            or die "can't open $ftpoutbound :$!";
while (<$f>)
{
    chomp;
    my @ftp_fields = split /;/;
    if (exists $data{$ftp_fields[0]}) {
        $data{$ftp_fields[0]}{TRANSPORT} = $ftp_fields[7];
    }
}
undef $f;

# display the results
foreach (sort keys %data)
{
    printf "%s|%s|%s\n", $_, $data{$_}{COUNT}, $data{$_}{TRANSPORT};
}

sub usage
{
    print <<EOL
Usage:
This program requires one argument, w/ an optional help argument.
Options should be specified as follows:
-d|date       OPTIONAL    Takes in the mmddyyyy format only.
-p|path       OPTIONAL    Specifies a particular path.
-h|help       OPTIONAL    Prints this message.
example: ./TransactionsPerDay.pl --date 09152003
EOL
;
    exit(1);
}
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Note that I have added the Data::Dumper module in the code to inspect the structure of the hash table. I haven't tested the code, but I am confident that it would work. :-D