I'm not a sysadmin guy at all so I have no content feedback but I can suggest a little style to make this sort of script more maintainable and easier to read. So a big bunch of printing from your script looks like this-

sub line { ( "*" x 70 ) . "\n" }

print join("\n",
           line(),
           $header,
           $allowedUsers,
           $permitRootLogin,
           $permitEmptyPasswords,
           $protocol,
           $ignore,
           $client,
           $allowedUsers,
           line()
          );
# Update: I know someone will suggest it if I don't.
# Instead of "sub line" you could do-
#   use constant LINE => ( "*" x 70 ) . "\n";
#      -or-
#   my $Line = ( "*" x 70 ) . "\n";
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Though if this is something you really care about, I'd skip this intermediate step and use Template. Then you could have a plain text/terminal template, an HTML template, and whatever subsets you wanted.