Strange solution, I have been unsuccessful (file name is created, but 0 bytes) trying to pass the image file name as a scalar into an upload subroutine, as in your example

my $filename = $q->param('filename');
&uploadFile($filename);

sub uploadFile {
    my $file = shift;
    ...
[download]

and found success only in grabbing it within the subroutine itself.

sub uploadFile {
    my $file = $q->param('filename');
    ...
[download]

And I'm not really sure why. But I'd thought I'd add this to the discussion in hopes to better understand the process.