In Mojave I face the same problem where the Hydro cooler usb was plugged into the motherboard usb header and would prevent sleep. This was solved by adding uia_exclude=HS14 to the boot argument, this argument is now added to the DSDT. On my rig everything works as it should, sleep/wake, iMsg/T-Time, Apple TV etc, etc.
If everything is working, do a full back up of the system including the EFI Partition on a spare disk so you can get back to a working system, then download the App Hackintool and have a go at mapping your own USB ports, the process is super simple and once done, you won't ever have to go through the process of port mapping on that board again.