Thank you RehabMan. I saw this guide but didn't use it. I was confused because it's listed as "mojave laptop" guides (I'm on High Sierra and desktop) and didn't want to break my system. I was coming back to update my post that I seemed to have fixed it, but I'm not 100% sure on that.
This is how I fixed it, but was hoping to confirm I went about this the correct way. I read in Clover Configurator that USBInjectAll.kext was to be used temporarily. Is it not something you keep on your system? I still have it there. Do I need to remove it?
To get this working, this is what I did.
1. Ran Multibeast for HS and added the USBInjectAll.kext
This finally stopped my external hard drives as being recognized as internal drives.
2. But, then I couldn't plug in more than one USB thing (disk or flash drive) at a time.
So I applied this patch:
https://www.tonymacx86.com/threads/new-usb-raise-port-limit-patch-for-high-sierra.226072/
3. With this I got USB 2.0 working but not 3.0
So I applied this patch:
https://www.tonymacx86.com/threads/...h-for-high-sierra.226072/page-12#post-1755102
And this gave me USB 3.0.
All seems to be working well for now. Initially, around step two my Apple Watch unlock stopped working if a USB was plugged in but that seems to have stopped now. I've had several successful Apple Watch unlocks from sleep.
Have I gone about doing this correctly or should I undo everything I did and follow the guide you linked.