open TWO, '<', $FILE2;        # better be explicit ;-)
    while (<TWO>)
    {
        chomp;                    # correct indent level is here.
        my ($key,$value) = split /\s+/,$_;
        print "$key NOT IN FILE 1\n" unless $hash1{$key};
        $hash2{$key} = $value;
    }

##</code><code>##

foreach my $key (keys %hash1)
{
    if(exists($hash2{$key})
    {
        if($hash1{$key} == $hash2{$key})    # '==' if numeric, 'eq' if string
        {
            ...
        }
        else 
        {
            ...
        }
    }
    else    # this is the case you missed - $key not in file2
    {
        ...
    }
}