Regarding changing the USB ports to a different one that supports USB 3.0. I believe it's not possible without losing some functionality, the USB module connects directly to the aux module. I believe the USB module is also what allows CarPlay to work, so if you changed it to just a USB 3.0 I think you'll lose CarPlay and the aux.
Here's my post on replacing the USB module with a OEM one
Here's images of the module itself and its casing
Here's images of the boards inside