Families of Variable Names

The main loop of the program is now small enough to see all at once:

     while (<INFILE2>) {
       chomp;
       $ct_scanout = 1 if (/apply\s*\"grp[0-9]_unload\"/);
       $chain_test=1  if (/CHAIN_TEST/);

       if (( /\t*chain\s+\"chain([0-9])\"/) && ($chain_test)) {
         $chain_number = $1;
         &cleanup;
         $chain_input = (split /=/,$_)[1];
         $chain_input =~ tr/\"//d;
         $chain[$chain_number] = [split //, $chain_input];
         &printout if $chain_number == 7;
       }
     }                               #end of While statement

We can get rid of that end of While statement comment
Such comments are red flags
They suggest that your blocks are too long or too complicated
- (Or that they are poorly indented)