When what I want is 
+----+----+----+----+
|1   |2   |3   |4   |
|    |    |    |    |
|    |    |    |    |
+----+----+----+----+
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Well, you'll need somthing like:

 while ($boxLine =~ s/(\.+)/sprintf("%-*d", length($1), $wordNum)/e) {
   $wordNum++
 }
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But then you'll have to skip over the other lines which have blanks (you have multiple lines per square).