By 'inner block' do you mean this:

  while (my $line = readline(SORTD)) {
    my $number = substr($line, $i*2, 2);
  }
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If so, I don't see where you are incrementing $i.

The way the for loop works is that $i will not be incremented until the end of the for block is encountered, so $i is not going to be incremented inside the while loop unless you explicitly do it yourself.