I'm back.
Thought I'd start from scratch.
I have spent the morning doing a fresh install of High Sierra (10.13.6) onto a spare SSD. Multibeast was used only for the bare essentials (Clover, eSATA, NullCPUPowerManagement, FakeSMC and network drivers) Nothing USB was selected.
I then proceeded to manually install USBInjectAll.kext and XHCI-unsupported.kext but NOT the port patch.
Following the guide I applied the -uia_exclude_hs uia_include=HS03,HS04 flag and rebooted. Using IORegistryExplorer I got the relevant SS port detail, then changed that flag to -uia_exclude_ss exclude=USR1,USR2 and got the relevant HS port details. Making notes all the time.
I then edited the SSDT-UIAC-ALL.dsl appropriately.
Following the instructions to the letter I created the AML file, placing it in /clover/acpi/patched, renaming it to SSDT-UIAC.aml
Still does not work. The HS side of things is fine, no USB3 (SS) ports are functioning.
I have included both the debug files PRIOR to SSDT creation and POST creation, thinking that you may see where I'm going wrong.
Again, thank you for you time.