Long list of remarks follows...

for my $arg (@ARGV) {
    #$script=$ARGV[0];
    #$stanza=$ARGV[1];
    $metricsfile=$ARGV[0];
    $resultfile=$ARGV[1];
    }
[download]

The for loop does nothing, remove it!

use strict;   # always!
use warnings; # always!
[download]

### Assigning the argument file to in_file ####
$in_file = $metricsfile;
[download]

No need for cmts that do not improve readability, and even degrade it. Well written code should be self explanatory.

Why assigning to yet another scalar and not using $metricsfile directly?

open (IN, "<$in_file") or die "Can't open $in_file: $!";
[download]

For the n-th time, n being a huge integer: you'd better use the 3-args form of open and lexical filehandles.

### A while condition to read all the lines in a file and place in an 
+array####
#my $linenum=1;

while(@linesFromMetrics=<IN>){ # opening while loop
[download]

NO! you either want

my @lines=<IN>;
# or
while (my $line=<IN>) { # ...
[download]

 #print "Reading metrics file \n";
 #print $linenum++;
[download]

You may be interested in $. - read more about in perldoc perlvar.

 ### Assigning the argument file to in_file ####
 $input_file = $resultfile;
[download]

Your comment is not consistent with your code in two ways: missing sigil and wrong variable name. One more reason not to have useless comments: if you change, say, a variable name, then you'll have to change the comment as well.

Well, that's kinda too much. I'll suggest you another way round - this assumes your files are reasonably sized:

#!/usr/bin/perl

use strict;
use warnings;

die "Usage: $0 <file1> <file2>\n" unless @ARGV==2;

my %orig=map {$_ => 1} do {
    open my $fh, '<', $ARGV[0] or die $!;
    <$fh>;
};

open my $fh, '<', $ARGV[1] or die $!;
$orig{$_} and print while <$fh>;
 
__END__
[download]

This is intendedly minimal: expand and adapt to your needs!

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