You definitely don't want to nest your file-reading loops. Instead, try something like this (untested): 
while (my $w1 = <FILE> and my $w2 = <FILE2>) {
  if ($w1 lt $w2) {
    print "\n";
    $w1 = <FILE>;
  }
  elsif ($w1 gt $wt) {
    print "\n";
    $w2 = <FILE2>;
  }
  else {
    print $w1;
  }
}
# Leftover lines in either file?
print "\n" while <FILE>;
print "\n" while <FILE2>;

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In reply to Re: Loop through 2 files in parallel by Roy Johnson
in thread Loop through 2 files in parallel by Anonymous Monk

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