I tried to generically connect via sqlite3 and was unsuccessful:

$ sqlite3 cert8.db
   SQLite version 3.3.6
   Enter ".help" for instructions
   sqlite> .tables
   Error: file is encrypted or is not a database
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I did some research and it appears that sqlite3 may not be able to communicate with the stored format. However, I think I did find a work around. Basically, if I use the strings command on the cert8.db file, it will dump the contents of the db file on different lines and I can find the certificate names alone on a single from there. So I updated my code to:

my %certs;
my @stored_certs;

# Get stored certificates:
my $command = "strings $config{firefox_profile}/cert8.db";
open(OUTPUT , "-|", "$command");
while (my $line = <OUTPUT>){
    chomp $line;
    if ($line =~ /CN=/i) {
        $line =~ s/^!//g;
        $line =~ s/(^\s+|\s+$)//g;
        if (! $certs{$line}) { $certs{$line}{stored_in_firefox}++; }
    }
}
close OUTPUT;

# Get each stores certificate's trust level:
$command  = "certutil -L -d $config{firefox_profile}";
open(OUTPUT, "-|", "$command");
while (my $line = <OUTPUT>){
    chomp $line;
    push (@stored_certs, $line);
}

foreach my $cert (sort keys %certs) {
    foreach my $line (@stored_certs) {
        if ($line =~ /^$cert/) {
            $line =~ s/^$cert//;
            $line =~ s/(^\s+|\s+$)//;
            $lcerts{$cert}{trust_level} = $line;
        }
    }
}
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I think this is good enough for now. Thanks again,