Ok here is my ioreg, but with ones are my 2 USB 3.1 ports? thanks
You're using the port limit patch. So first thing you need to do is eliminate unused/unneeded ports to get under the 15-port limit. You create a custom SSDT for USBInjectAll.kext to do that. It is covered in the guide I linked before...
It appears you tested 6 USB3 ports... SS01-SS06 with USB3 devices. But you didn't plug any USB2 devices into those ports, so you don't currently know which HSxx ports are associated (there will be one for each). But since you have 6 USB3 ports, that is 12 ports total (each USB3 port uses an HSxx and SSxx port, so two each). It means you can enable 3 more HSxx ports (associated with USB2-only ports/headers) and still stay within the 15 port limit. I see HS12, HS13, HS14 used/tested, so hopefully that is all you need... (plus the other 6 HSxx ports that are associated with the 6 SSxx ports, for a total of 6+6+3=15).
Also, if some of those SSxx ports are USB3.1, you need to set UsbConnector for them correctly (and UsbConnector for USB2-only HSxx should be 0). The ACPI 6.0 spec has some details on it (look at the table for _UPC). I don't have any experience with USB3.1 (type C) stuff, so you're on your own in reading the info in the ACPI spec... According to the spec, USB type C, comes in three flavors 0x08, 0x09, 0x0a... so you will want to read the relevant section of the spec.
Here is the relevant data from the spec:
0x08: Type C connector - USB2 USB2-only receptacles
These only implement the USB2 signal pair, and do not implement the SS signal pairs.
0x09: Type C connector - USB2 and SS with Switch receptacles
These implement the USB2 signal pair, and a Functional Switch with a physical Multiplexer that is used to dynamically connect one of the two receptacle SuperSpeed signal pairs to a single USB Host Controller port as function of the Type-C plug orientation.
0x0a: Type C connector - USB2 and SS without Switch receptacles
These implement the USB2 signal pair and a Functional Switch by connecting each
receptacle SuperSpeed signal pair to a separate USB Host Controller port.
I suspect the most common would be 0x09 (hopefully... otherwise each of those ports uses two SSxx and one HSxx). You will find out when you turn the connector upside down and see if a USB3 device connects to a different SSxx port depending on orientation. If it connected to a different SSxx port depending on orientation, it would be a 0x0a. At least that's how I read it...
I didn't look at EFI.zip. It is too large. The request was not for EFI at all. It was for only EFI/Clover (stripped of themes).
And you didn't provide the other data requested (various kextstat and kextcache output).
USB is unreliable if you have more than 15 ports enabled. So, you definitely want to set it up so that you're at or under 15 and without the port limit patch.