Hi pli, I am glad it was a good starting point for you!
I can see that you have already implemented Emulated NVRAM (EmuVariableUefi-64.efi) It means Non Volatile Random Access Memory, it stores information like OS parameters, volume, brightness (laptops) amongst many other things for the next boot up. Your emulated nvram.plist is in your EFI partition (As you don't have native/hardware NVRAM supported by macOS).
I also have been testing, tweaking, adding/changing hardware and discovering new things. When i added the thunderbolt ex3 card i had the same issues as you mentioned about not booting every time. OsxAptioFixDrv-64 fixed it and everything was really smooth UNTIL... I tried to enabled IGPU (headless mode for Mojave) and then things went bad and had to boot from a backup and reinstall clover bootloader.
The fix for me was OsxAptioFix2Drv-free2000 and slide=0 in clover boot options. Thank you to
@CaseySJ thread
https://www.tonymacx86.com/threads/success-ongoing-status-of-designare-z390-with-i7-9700k.266065/ and
https://www.tonymacx86.com/threads/...nare-z390-thunderbolt-3-with-i7-9700k.267551/
Even though its a Gigabyte motherboard, its still a Z390 chipset, so some things will apply to us also.
You will probably be fine on High Sierra though and won't need IGPU at all, but OsxAptioFix2Drv-free2000 and slide=0 might be something to test, especially if you add more PCIE devices. Works a treat for me!
You should also implement your USB's and AppleBusPowerController as you are still using the patch. It's really easy once you have done it once and it makes such a positive impact on system stability
I will upload my latest clover folder when i get back to the studio and i will include a SSDT-UIAC.dsl template for you to edit.