assuming you want any missing letter in the well defined sequence A-Z in either file to be printed as a blank line. untested 
@arr1=<FILE>;
@arr2=<FILE2>;
for $letter(A..Z) {
 if(grep($letter, @arr1) or grep($letter,@arr2) {
   print "$letter"
 }
 print "\n";
}

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the hardest line to type correctly is: stty erase ^H

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

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