open(IN, "<temp.in") || die "\n Can't open file\n $!\n";
open(OUT,">temp.out");

   ## Search for FTN
   my %values;

   # read through the input fileto get the values
   while(<IN>) {
      if(/<FTN ID="FN(\d{3})">(.+?)<\/FTN>/) { #no need to quote <, >, ", =
         $values{$1} = $2;
      }
   }
   close(IN);

   open(IN, "<temp.in") || die "\n Can't open file\n $!\n";

    ## replace X-REF
    while(<IN> ) {
       s/<FTN.+?<\/FTN>//; # get rid of existing <FTN> tags - we already have the values from them
       s/(<X-REF REFID="FN(\d{3})">.*)(<\/X-REF>)/$1<FTN>$values{$2}<\/FTN>$3/; # alter the X-REF LINE
       print OUT;
    }

close(IN);
close(OUT);