For that CPU, make sure you update Clover to rev 3727 or newer, because there was a bus frequency detection bug.
USB 3 worked for me OOTB with Apple's XHCI driver. In the BIOS, XHCI mode should be enabled.
I haven't tried any NVMe stuff.
What's the problem with audio? If it's crackly, that will be fixed with the Clover update. I'm using VoodooHDA now, but I am going to try switching to AppleHDA soon, because the sound quality is not great.
Here is my EFI folder.
https://drive.google.com/open?id=0B52QuT8oHvtZdWtfazVNeVQ3Qlk