Your spec is ill defined - please read I know what I mean. Why don't you?. Specifically, please give us concrete examples of input and output. You say you "can split & iterate though, and get it working", so the easiest way to help us understand what you need is to post code the does what you need. From there, we can critique the code and help you improve your skill with and understanding of Perl.

Update: With your updated node, I can provide some more useful suggestions. You can accomplish your mapping using the code posted in Limbic~Region's subthread, so the smallest mod to your script the produces your desired result might look like:

#!/usr/bin/perl -w
#<UnusedGrp.pl> Find unused Groups in /etc/group

my $GROUPfile="/etc/group";
my $gfpid = open(GFILE, "<$GROUPfile") or die "$GROUPfile File Not Fou
+nd: $!\n";
my $PASSWD="/etc/passwd";
my $pfpid = open(PFILE, "<$PASSWD") or die "$PASSWD File Not Found: $!
+\n";
@PWLINES = <PFILE>;

while (my $line = <GFILE>) {
   @GRP = split(/:/, $line);
   if (length($GRP[3]) < 2){
     print "$GRP[0]:$GRP[2] is zero length\n";

     my @GIDs = map { (split /:/)[3] } @PWLINES;
     my $seen = 0;
     for my $GID (@GIDs) {
        if ($GID == $GRP[2]) {
           $seen = 1
        }
     }
     if (not $seen) {
        print "$GRP[0]:$GRP[2] has no users\n";
     }
   }
}
[download]

However, I would approach this problem a little differently. Given that you want to repeatedly check against the presence of a foreign key, the best approach here is Perl is usually using a hash. I would also use next for Loop Control rather than nested conditionals. My solution would look more like:

#!/usr/bin/perl -w
#<UnusedGrp.pl> Find unused Groups in /etc/group
use strict;

my $GROUPfile="/etc/group";
my $gfpid = open(GFILE, "<", $GROUPfile) or die "$GROUPfile Open faile
+d: $!\n";
my $PASSWD="/etc/passwd";
my $pfpid = open(PFILE, "<", $PASSWD) or die "$PASSWD Open failed: $!\
+n";

my %gids;
while (my $line = <PFILE>) {
    my @user = split /:/, $line;
    $gids{$user[3]}++;
}


while (my $line = <GFILE>) {
   my @GRP = split(/:/, $line);

   if (length $GRP[3] > 1) { # $GRP[0]:$GRP[2] is not zero length
      next;
   }

   if ($gids{$GRP[2]}) { # GID found in passwd
      next;
   }

   print "$GRP[0] has no users and no GID references\n"
}
[download]

though my final solution would probably be

#!/usr/bin/perl -w
#<UnusedGrp.pl> Find unused Groups in /etc/group
use strict;

my $GROUPfile="/etc/group";
my $PASSWD="/etc/passwd";

open my $gh, "<", $GROUPfile or die "$GROUPfile Open failed: $!\n";
open my $ph , "<", $PASSWD or die "$PASSWD Open failed: $!\n";

my %gids = map { (split /:/)[3] => 1 } <$ph>;

while (<$gh>) {
    my @fields = split /:/;

    next if length $fields[3] > 1;
    next if $gids{$fields[2]};
    print "$fields[0] has no users and no GID references\n"
}
[download]

I'll be happy to go over any questions you have about the above code. In particular, see Use strict warnings and diagnostics or die (or The strictures, according to Seuss).