Verify Clover settings are correct if Windows on the secondary drive is a legacy installation with bootloader installed in the MBR. Otherwise...
You can boot from EFI Windows installation media, then reinstall the windows bootloader (press Shift + F10 for a command prompt from installer...
From Windows you can use the free trial of EasyUEFI to add Clover to the firmware boot menu. Renaming Windows boot files to fix the boot order is a waste of time.
If you now have more than 4 working ports I'd guess "3rd Party USB 3.0" (whatever that is, probably installs GenericUSBXHCI.kext kext) has had an effect.
It looks like all your chipset ports are on 4 internal headers (3 x 2.0 and 1 x 3.0) + PCI/bluetooth while the I/O back panel ports are all on the unsupported Renesas uPD720210. Maybe you were using GenericUSBXHCI.kext previously?
Optimus is known not to work unfortunately, there is plenty of discussion on this forum. If you have Thunderbolt and an enclosure, EGPU is a possibility, recommend supported AMD GPU if you go down that road.
I think it is unlikely to work in a straightforward way, whether it will never work in any way i couldn't tell you. I know there is unofficial NVIDIA EGPU support with the web drivers on High Sierra, but on a laptop you may have additional software switching of the device thats not going to...
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