I too have tried to successfully implement robust file uploading with mod_perl. I failed.

This is why it's still handy to have a cgi-bin directory, which i what i use to solve this problem - a CGI script. Something like the following should get you started. I store the files in another directory outside of the cgi-bin dir, say UPLOAD (caps for emphasis only).

use strict;
use warnings;
use CGI qw(:standard);
use CGI::Carp qw(fatalsToBrowser);
use File::Basename;

my $PATH = '/path/to/upload/not/in/cgi-bin/UPLOAD';

print header, start_html('not very safe uploader');

if (param('go')) {
   my $handle = upload('the_file');
   my $name   = param('the_file');
   open OUT, '>', "$PATH/$name" or die "can't open target $name: $!";
   print OUT while <$handle>;
}

my @file = map basename($_), <$PATH/*>;

print start_multipart_form(),
   p('upload:', filefield('the_file',undef,50,80)),
   p(submit('go')),
   end_form,
   hr,
   ul(li[ map a({href=>"/UPLOAD/$_"},$_), @file ]), # YMMV here
   hr,
   end_html,
;
[download]

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)