Like this?

my $num;

while (<FILE>) {
   chomp;

   if ($. % 3 == 1) {
      $num = sprintf("%02d", rand(100));
      substr($_, 0, 2, $num);
   } else {
      substr($_, 1, 2, $num);
      substr($_, -2, 2, sprintf("%02d", rand(100)));
   }

   print("$_\n");
}
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If the line terminator is one character long, the above is simplifies to:

my $num;

while (<FILE>) {
   if ($. % 3 == 1) {
      $num = sprintf("%02d", rand(100));
      substr($_, 0, 2, $num);
   } else {
      substr($_, 1, 2, $num);
      substr($_, -3, 2, sprintf("%02d", rand(100)));
   }

   print;
}
[download]