`printout`

It's easy to make the globals into parameters:

      sub printout {
        my ($scanout, @chain) = @_;
        for my $i (0 .. $#{$chain[1]}){
          my $chars = "";
          for (@chain) { 
            next unless defined;
            $chars .= $_->[$i];
          }
          if ($scanout) {
            $chars =~ tr/01/LH/; 
          } else {
            $chars =~ tr/X/0/;
          }
          print OUTFILE 
            $scanout ? "\n(ct_so\n" : "\n(ct_si  $ct_si{tdi}\n",
              "$chars\n )";
        }
      }

In the main loop, the call becomes:

      printout($ct_scanout, @chain) if $1 == 7;