I still see the uprid added to the end with file caching turned on in my test environments (and on your site). From what I've read this is normal behavior for the shopping cart page.
Just because you are redirected to the URL does not mean the URLs are being re-written inside Zen Cart. I suspect something is not quite right with the installation of this module in your site. I'd especially double check the auto-loader file and the zen_href_link function changes.
I'm not sure what stock-by-attributes changes, but the changes made for this plugin to functions_general are to remove the main_page parameter and add an XSS fix. These changes on the admin side should not affect the catalog side (they are not used by the catalog side).
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