Hi,
I am from the Softaculous team.
Sorry for the inconvenience caused. We have tested the WHMCS upgrade on several test servers and it worked fine.
If you can open a support ticket with us we will check it asap.
>> When I attempt to run the install script I get a WordPress 404 page not found. I am not integrating WHMCS with WordPress it's simply installed under the same URL.
It could be due to a .htaccess file in the root of your domain which is not allowing access to your WHMCS installation in a sub-directory.