There are many things that can slow your script down. As others have said usually 5% of the code consumes 90% of the execution time. The trick is to identify where those key routines are and look at ways to speed them up.

I have used tricks like caching results that can have a significant effect:

sub routine1
  {
    my($arg1,$arg2) = @_;
      ...
    return $result;
  }
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Is changed to:

{
  my %cached_results;

sub routine1
  {
    my($arg1,$arg2) = @_;
    return $cached_results{"$arg1||$arg2"}
            if(defined $cached_results{"$arg1||$arg2"});
      ...
    $cached_results{"$arg1||$arg2"} = $result;
    return $result;
  }

sub clear_cache1
  {
    %cached_results = ();
  }
}
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I recently had a case where I was using .= to build up a string, converting the routine to pushing strings on to and array and only concatenating at the end of the function reduced memory usage by a factor of 100 and increased speed by a factor of 10 for that one routine.

It is not worth hand coding modules in C until you have tried these types of tricks. The extra maintenance cost will swamp the benefit of speed you get.