while (
  defined(my $line1=<$file1>) and defined(my $line2=<$file2>)
 ) {
 if (abs(
   (split"\t",$line1)[2]-(split"\t",$line2)[2]
  )>=2) {
  print $w1 "$line1\n";
  print $w2 "$line2\n";
 }
}