The script assumes the same number of words in each file, since you showed the same number words in the two different word sets. Your next step is to make a few changes to adapt this script to handle files with different numbers of words.

I am comparing two files using hash and then checking each character by character.But even now when the position of the words are altered or some words are deleted from either files the error uninitialised value is coming

The script that you write needs to insure that only matching words are compared for difference. You can place the code that inserts a "+" at the first string difference position into a subroutine that can be called from anywhere within your script. For example:

use strict;
use warnings;

my $string1 = 'amayaM';
my $string2 = 'amayamAn';

my $result = firstStrDiff( $string1, $string2 );

print $result, "\n";

sub firstStrDiff {
    my ( $s1, $s2 ) = @_;

    ( $s1 ^ $s2 ) =~ /[^\x00]/;
    substr( $s2, $-[0], 0 ) = '+' if defined $-[0];
    return $s2;
}
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Output:

amaya+mAn
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This can help you focus on just the remaining code that aligns the words you want send to this subroutine.

Hope this helps!