From the documentation of Apache2::Request:

upload

    $req->upload()
    $req->upload($name)
[download]

With no arguments, this method returns an APR::Request::Param::Table object in scalar context, or the names of all Apache2::Upload objects in list context.

So, your $upload loop variable contains just a string (the name of an Apache2::Upload object). The string is no object proper, so you can't $upload->fh. Not having used myself anything mod_perl or Apache2::whatever - perhaps the following works:

foreach my $upload ($r->upload()) {
        my $upload_fh = $r->upload($upload)->fh;
        my $contents;

        while(<$upload_fh>) {
                $contents .= $_;
        }
        close($upload_fh);

        # write $contents to the file here...
}
[download]

_($_=" "x(1<<5)."?\n".q·/)Oo.  G°\        /
                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}