A       crap
B       crap
C       crap
D       crap
E       crap

##</code><code>##

A       crap    B       C       crap    D       crap    crap    E
1       2       3       4       5       6       7       8       9
11      12      13      14      15      16      17      18      19
21      22      23      24      25      26      27      28      29

##</code><code>##

open IN, "<file1" or die $!;
while(<IN>){
        $sID{$1} = 1 if /^(\w+)\t/;
}
close IN;

open IN, "<file2" or die $!;
map {$i++; push @cols, $i-1 if exists $sID{$_}} split(/\t|$/, <IN>);
while(@a = split /\t|$/, <IN>){
        print join "\t", @a[@cols],"\n";
}
close IN;

##</code><code>##

1       3       4       6       9
11      13      14      16      19
21      23      24      26      29