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...
Look at the IOService tree, you should see your graphics card on one of the PCI ports with or without NVDA-prefixed classes depending on whether NVIDIA drivers are loading. For NVIDIA device, search for 'display'
edit: see also the GUI app IORegistryExplorer, its attached to this post
Inject Nvidia should be unchecked.
In NVIDIA system preferences pane there is an option to uninstall the driver.
If you're using a laptop, configuring the discrete card for macOS may not be so straightforward in any case. Maybe use IORegistry Explorer to see what, if any display devices are...
With SIP disabled, when the kernel cache was rebuilt after installing the NVIDIA drivers any unsigned kexts installed to /Library/Extensions will have been excluded.
You can configure Clover on a per-boot basis by pressing 'o' for options at the boot menu e.g. enable the NvidiaWeb function...
In config.plist specify DefaultVolume, you can use the GPT partition UUID. For volumes with multiple loaders also specify DefaultLoader, you can use the path to Windows bootloader e.g. \EFI\Microsoft\Boot\bootmgfw.efi
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