This should do:

my $old_parent = $root;
my $new_parent;
my %modules;

for my $node ($old_parent->childNodes()) {
    next if $node->nodeName() ne 'module';
    my $mod_name = $node->getAttribute('name');
    if ($mod_name eq 'all') {
        $new_parent = $node;
    } else {
        $old_parent->removeChild($node);
        $modules{$name} = $node;
    }
}

my %refcount;
for my $node ($new_parent->childNodes()) {
    next if $node->nodeName() ne 'moduleref';
    my $mod_name = $node->getAttribute('name');
    my $referred_node = $modules{$name}
        or next;
    $referred_node = $referred_node->cloneNode(1)
        if $refcount{$mod_name}++;
    $new_parent->replaceChild($referred_node, $node);
}
[download]

A bit or error checking is needed. You didn't specify what you wanted to do with the modules that aren't referenced. The above removes them.