Quick update: I have everything working now (I think)... Except for audio!
I used your latest EFI, as I didn't have any port limit patches in my config.plist to disable... I probably did something wrong at some point! Once your EFI was in, I can see your port limit patches and they're disabled. So all the USB ports are working now - aside from the USB type C, and the port directly above it, which is expected with your SSDT. I think in future I'd like to get those two working, and can presumably swap out something else like the RGBs, as you've mentioned before.
I got the graphics glitches again, so I did what I did before and changed the SMBIOS back to iMac(14,2) using MultiBeast, and that fixed it. I used Intel Power Gadget to verify hardware acceleration was working,
using this post, and everything looked fine (on my i7-8700, HD630).
Interesting point about audio not working with the integrated graphics enabled. I have the common issue of no audio devices detected at all, but my two folders (EFI/Clover/kexts/Other and System/Library/Extensions) look identical to yours, aside from missing a couple of unrelated kexts you have.
I've read a few posts about the audio,
such as this, but don't really understand what I'm doing with it. Also I note that's for AppleHDA, and I have AppleALC.kext . . . I don't understand the difference!