Hello,
I've got the same Motherboard as you and I'm having some issues with my USB-C Ports, they don't seem to work both ways. USB-C is meant to be reversible and when I plug in a USB3 Flash Drive via an Apple USB-C to USB Type-A Adaptor, I plug into Port 01 which is closest to my DP In and USB-C Works, I flip the plug and plug it in upside down and it works. I move over to Port 02 which is closest to HDMI, I plug it in and it doesn't work, I plug it in upside down and it works. I have replicated Port 02 not working when plugged in right way up on both Windows 10 64 Bit and macOS 10.12.3. Can you verify if you have similar problems when reversing the cable?
Also, when you say:
'If anyone has read up on successful USB-C/TB3 builds, they require a driver to be installed on a Windows partition that activates the port on your Z170 board. Once this is worked out, you may use USB-C devices on your CustoMac.'
Are you referencing the TB Firmware Update? I've done that but I wasn't too sure if it was for TB only or TB/USB-C.