`Making Two Passes`

Here we're making two passes over @chain:

      for (@chain) { 
        if ($ct_scanout ) {
          $_->[$i] =~ s/0/L/g; 
          $_->[$i] =~ s/1/H/g;
        } elsif ($ct_scanout==0) {
          $_->[$i] =~ s/X/0/g;
        }
      }
      my @chars = map $_->[$i], @chain;

"Do I really need two passes?"
"Or could I do both transformations in one pass?"
Yes:

      my @chars;
      for (@chain) { 
        if ($ct_scanout ) {
          $_->[$i] =~ s/0/L/g; 
          $_->[$i] =~ s/1/H/g;
        } elsif ($ct_scanout == 0) {
          $_->[$i] =~ s/X/0/g;
        }
        push @chars, $_->[$i];
      }