use strict;
use warnings;

use XML::LibXML qw( );

die "Usage" if @ARGV != 3;

my $parser = XML::LibXML->new();

my @counts;
{
   my $doc = $parser->parse_file($ARGV[1]);
   my $root = $doc->documentElement();
   @counts = map $_->textContent, $root->findnodes('elem');
}

{
   my $doc = $parser->parse_file($ARGV[0]);
   my $root = $doc->documentElement();
   for my $node ($root->findnodes('elem')) {
      die "Not enough counts" if !@counts;
      $node->appendText(
         $node->textContent() x (shift(@counts) - 1)
      );
   }

   print $doc->toFile($ARGV[2]);
}

die "Too many counts" if @counts;
[download]

Or if counts of 0 are acceptable:

      my $new_text = $node->textContent() x shift(@counts);
      $node->removeChild($_) for $node->findnodes('text()');
      $node->appendText($new_text);
[download]

Tested.