here is something I've tried to make out of your code.
I hope, that helps a bit :-))
The vars ending with usr_specific I left empty, so the produced script will redirect to your localhosts root dir when that blank.

#!/usr/bin/perl -w
use strict;
$|++;

use CGI qw/:all /;
use CGI::Carp qq/fatalsToBrowser/;

my ($q, $basedir, $q_brieftitle, @stored, @output, $line, $rights);
my ($dir_usr_specific, $rights_usr_specific, $filetypes_usr_specific, 
+$domain_usr_specific);
$q = CGI->new();
print $q->header();
print $q->start_html();

#####Create Perl upload script

$basedir = "..";
$q_brieftitle = "/cgi-bin";
# user sepcific definitions go here
$rights = '$basedir = "/home/sites/stuff/users/'.$dir_usr_specific.'";
+';
$rights .= '$allowall = "'.$rights_usr_specific.'";';
$rights .= '$theext = ".'.$filetypes_usr_specific.'";';
$rights .= '$donepage = "'.$domain_usr_specific.'";';
# end user sepcific definitions

open (FILE, ">$basedir$q_brieftitle/upload.cgi") || die "blah";
#flock(FILE, 2);

# process
@stored = <DATA>;
foreach $line (@stored)
{
    push @output, $line;
    if ($line =~ /^\# usr_spec_def/i)
    {
        foreach $_ (split (";", $rights))
        {
            push @output, $_.";\n";
        }
    }
}

print FILE @output;
close FILE;

print $q->code(pre(@output)), end_html();

# the folllowing DATA section could also be somewhere in a file
__DATA__
#!/usr/bin/perl
use strict;
$|++;
use CGI qw/:all/;
my ($basedir, $allowall, $theext, $donepage, $req, $onnum);
## DO NOT EDIT OR COPY ABOVE THIS LINE :-) ##
# usr_spec_def
## DO NOT EDIT OR COPY BELOW THIS LINE##  

$req = CGI->new();
$onnum = 1;
while ($onnum != 11)
{
    my ($bytesread, $buffer, $filenotgood);
    my $file = $req->param("FILE$onnum");
    if ($file)
    {
        my $fileName = $file;
        $fileName =~ s!^.*(\|\/)!!;
        my $newmain = $fileName;
        if ($allowall ne "yes")
        {
            if (lc(substr($newmain,length($newmain) - 4,4)) ne $theext
+)
            {
                $filenotgood = "yes";
            }
        }
        if ($filenotgood ne "yes")
        {
            open (OUTFILE, ">$basedir/$fileName") || die "failed";
            print $req->p("$basedir/$fileName");
            while ($bytesread = read($file, $buffer, 1024))
            {
                print OUTFILE $buffer;
            }
             close OUTFILE;
         }
    }
     $onnum++;
} 
print $req->redirect($donepage);
[download]

when I was looking on your code, it was quite helpful to me, that this one gives the content of the created file to the browser(screen).
I hope by now, I understood, what you are trying to do :-))
have a nice day

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