I'm not entirely sure if this would be the optimal solution in your case, but the way I think this might work is if you were to fork off a child process to handle the file writing part. This would allow you to free up the main process to finish rendering the page to the web client and thereby avoid the time out message.

The code might look something like this (not tested! :):

if (!fork) { # doing stuff in child process...
  # open your file handle here
  while (my $bytesread = read($filesource, my $buffer,1024)) 
  {
    print OUTFILE $buffer;
  } 
  # you could also write to a 'status' file and display that back to t
+he client ;)
  exit; 
}

print $cgi->header();
print "Your upload is in process... see this status.html page for the 
+status (changes every once in awhile :)\n";
exit;
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_____________________

$"=q;grep;;$,=q"grep";for(`find . -name ".saves*~"`){s;$/;;;/(.*-(\d+)
+-.*)$/;
$_=["ps -e -o pid | "," $2 | "," -v "," "];`@$_`?{print"+ $1"}:{print"
+- $1"}&&`rm $1`;
print$\;}
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