#!/usr/local/bin/perl -wT

use strict;

my($putNum,$line,$s_count,$num,$n_line, @square);

$putNum = 1;

@square = (
   '+----+',
   '|....|',
   '|....|',
   '|....|',
   '+----+'
);

foreach $line (@square) {

   if (!$putNum) {
      $line =~ s/\./ /g;

   } else {

      if ($line =~ /\./) {
         $s_count = $line =~ s/\./\./g;

         $num++ if ($s_count);

         $n_line = "$num" . ' ' x ($s_count - length($num));

         $line =~ s/\.+/$n_line/o;
      }
   }

   print "$line\n";
}

# OUTPUT

+----+
|1   |
|2   |
|3   |
+----+
[download]

I solved the 1st problem you rose when $putNum is decided. If the line being considered is either the top or bottom line, $putNum is false.

As to your second point, tmtowtdi. ;-)

But I see I still haven't been clear. :-(
the output I'm seeing is

+----+----+----+----+
|1   |1   |1   |1   |
|    |    |    |    |
|    |    |    |    |
+----+----+----+----+
[download]

When what I want is

+----+----+----+----+
|1   |2   |3   |4   |
|    |    |    |    |
|    |    |    |    |
+----+----+----+----+
[download]

Update:
Take a look at my scratch pad for the full code

print join("\n", @empty_square), "\n";

+----+
|2   |
|3   |
|4   |
+----+
[download]