
Let me look at the structure a second.

The problem you have is that your shop is publishing an index.php to your mydomain.com/shop and your doing the same thing as far as I can tell through wordpress so it's being overwritten. Which one shows depends on the last one published. I would think you could do a redirect script to send user to the correct page.
It's easy to overlook something you're not looking for.
This is a site I built for my work.(RSD)
http://esmansgreenhouse.com
This is a site I built for use in my job.(HTML Editor)
https://pestlogbook.com
This is my personal site used for testing and as an easy way to share photos.(RLM imported to RSD)
https://ericrohloff.com