May be you can try to read data in hash first as it is an index data, then match key to it and add the value. I am assuming your master data in the format that you have provided.

#!/usr/bin/perl -w
use strict;

my $file1 = "file1.txt";
my $file2 = "file2.txt";
my %hash = ();
my %ahash = ();

open F1, $file1 or die "Can't open $file1 $!";
open F2, $file2 or die "Can't open $file2 $!";

while(<F1>){
        my $line = $_;
        chomp($line);
        $hash{$line} = $line;
}

while(<F2>){
        my $line = $_;
        chomp($line);
        (my $w1, my $w2) = split(/ +/, $line);
        $ahash{$w1} = $w2;
}
# Matching of two Hash
for ( keys %hash ) {
    unless ( exists $ahash{$_} ) {
        print "$_: not found in second hash\n";
        next;
    }

    if ( $hash{$_} eq $ahash{$_} ) {
        print "$_: values are equal\n";
        # Do something with the value
    }
    else {
        print "$_: values are not equal\n";
    }
}
[download]

Might be it will give you an idea to compare files data using hash.