Thanks for the answers and comments so far.
I did test all the suggestions too, and I found that the things were worsening about 20% (no profiles, I still have to learn that, just used ps...) with:
1. use of unpack (quite clean coding though)
2. extracting the strings from $record and "printing" the exponetial format with, more or less, this code:

...
   foreach $it (1..$nt) {
      $x11 = substr($record,$lmina,1);
      $x12 = substr($record,$lmina+1,4);
      $ib = substr($record,$lminb,2);
      if ($x11 ==  0 and $x12 == 0 and $ib == 99) {
         $values[$it-1] = $val_missing;
      } else {
         if (($ib % 2) == 0) {
            $x2 = $ib/2;
         } else {
            $x2 = -($ib+1)/2;
         }
         $values[$it-1] = sprintf "%u.%4.4uE%3.3d\n",$x11,$x12,$x2;
      }
      $lmina = $lmina + 5;
      $lminb = $lminb + 2;
   }
   return @values;
}
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There is a 20% improvement by removing the subtractions when indexing (avoiding things like $values[$it-1])
There is no gain by preparing a @tmp array and make just one printing per record
Roberto