Show some sample input and expected output? Also, don't throw everything at Perl at once in frustration and hope something sticks, break the code down into small bits and test each part and print debug stuff for each, Data::Dumper is your friend. Basic debugging checklist

If you don't get @ARGV then don't use it, magic <> isn't the only way to read files, when in doubt spell it out:

my @file_list = ( "some_file", "other_file" );
push @file_list, "more_files", "and_more";
for my $file (@file_list) {
  open my $fh, '<', $file or die "$file: $!";
  while (my $line = <$fh>) {
    chomp $line;
    # ...
  }
  close $fh;
}
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And please don't define your vars before you need them - not my $i; ... for ($i=1;..., do for (my $i=1;... - makes the code hard to read, lots of distractions, and you'll have scoping problems later