This should get you started:

#! perl -slw
use strict;
use Inline::Files;
use Data::Dump qw[ pp ];

my @templateIds = split ' ', <TEMPLATE>;
my %template = map{ my( $id, @vals )= split(); $id => \@vals } <TEMPLA
+TE>;
#pp \%template;

my @missingIds = split ' ', <MISSING>;
my %missing = map{ my( $id, @vals )= split(); $id => \@vals } <MISSING
+>;
#pp \%missing;

for my $i ( 0 .. $#templateIds ) {
    if( $templateIds[ $i ] ne $missingIds[ $i ] ) {
        splice @missingIds, $i, 0, $templateIds[ $i ];
        for my $k ( keys %missing ) {
            splice @{ $missing{ $k } }, $i, 0, 0;
        }
        $missing{ $templateIds[ $i ] } = [ (0) x @{ $template{ $templa
+teIds[ $i ] } } ];
    }
}

print "\t", join ' ', @missingIds;
print join ' ', $_, @{ $missing{ $_ } } for @missingIds;


__TEMPLATE__
             rs12272511 rs7107801 rs11027752 rs12421837
rs12272511 1.0 -0.023 -0.511 -0.046
rs7107801 -0.023 1.0 0.040 0.233
rs11027752 0.494 0.514 1.0 0.501
rs12421837 -0.039 -0.040 0.021 1.0
__MISSING__
             rs12272511 rs11027752 rs12421837
rs12272511  1.0 .844 .276
rs11027752  .267 1.0 -.980
rs12421837 -.876 .374 1.0
[download]

Output:

C:\test>1152731
        rs12272511 rs7107801 rs11027752 rs12421837
rs12272511 1.0 0 .844 .276
rs7107801 0 0 0 0
rs11027752 .267 0 1.0 -.980
rs12421837 -.876 0 .374 1.0
[download]

Note:I've used Inline::Files to produce a self-contained example; you'd need to open the real files and operate on them for your real work.