ack! why use chop when you can use the safer chomp? And how come neither was used inside the while (<MAPFILE>)? Finally, why did you remove the call to lc?

# chomp the inputs to remove the trailing \n
chomp(my $l = <STDIN>);

.
.
.

# 3-arg open safer.
# No use putting quotes around $sdtfile.
open(MAPFILE, '<', $sdtfile)
or die("Unable to open map file: $!\n");

# No need to load whole file in memory.
# Use while instead of foreach.
while (<MAPFILE>) {
   my (
      $date,
      $time,
      $lot,
      $waf,
      $ts,
      $sstep,
      $machine,
      $prog,
      $product,
      $plnfile,
      $striping,
   ) = map lc, split(/,/, $_);

   if (...) {
      .
      .
      .
   }
}
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