After some feedback and research I've added a differential multiplexer that can handle USB 3.1 speeds to reduce reflections on the not connected SS-pairs. The MUX is controlled by the STM32 micro,  that can detected the cable orientation based on the CC pins. 

Also I removed the files from here and provided a link to the open gitlab project, where you can always find the latest files. The layout and schematic can also be viewed directly in the browser within the cadlab.io project.

If you have any feedback, I'd appreciate it very much. Ether leave it here or on the gitlab project.

Thanks - Jacky