Here's a few checks you could easily add:

• Was a file name entered?
• Does this file contain data?
• Is the data of the expected size/type/format?

It looks like you're assuming that it's a text file, and you read it into memory line by line. But what if someone accidentally sends you a large binary file (maybe it's the correct file, only it's been zipped)?

Here's a revised version of your upload() function that uses read() to read the file into a buffer 1kb at a time, and abort if it looks too big (you can set your own limit).

sub upload {
  my $self = shift;
  my $q = $self->query;
  if(untaintFile($q->param('file')) && $q->upload('file')) {
    my $filename=untaintFile($q->param('file'));
    ($filename) = $filename =~ /([[:ascii:]]+)/;

    unless($filename) {
      croak "no filename given!";
    }

    my $file = $q->upload('file');

    unless($file) {
      croak "can't get filehandle for upload!";
    }

    my $data;
    my $buffer;
    my $bytesread = 0;
    my $totalbytes = 0;

    while($bytesread = read($file, $buffer, 1024)) {
      $totalbytes += $bytesread;
      if($totalbytes > $MAX_DATA_LIMIT) {
        croak "upload file too big!";
      }
      $data .= $buffer;
    }

    unless ($data) {
      croak "no data!";
    } else {
      my $thisfile = File->parse($data);
                        
      if(my $format_error = $thisfile->check_formatting()) {
        # warn if any format errors found
      return;
                        }
      my $file_id = $self->file_upload({
        name => $filename, 
        data => $data,
      });
    }
  }
  $self->header_type('redirect');
  $self->header_props(-url => "$CONFIG{userbase}/user.pl");
  return;
}
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