No idea why you guys opened this thread separate from the X299 main threads. The necessary modifications for the ASUS Prime X299 Deluxe are also of interest for others. A simple post in one of the X299 main threads would have been helpful also for all others. I have seen the respective posts here with a delay of several days and weeks, because I even did not know that this thread exists at all. Ever heard about collaboration? My X299 threads are not only meant for taking but also for giving, even if one only returns feedback, remaining issues or some additional information.
You did not properly adopt SSDT-X299-TB3HP.aml, no surprise that it fails to load during system boot and in consequence TB is not properly implemented at all on your system. Please try SSDT-X299-TB3HP.aml attached below and report back with an IOREg.save and "PCI" snapshot of Apple's system report.It would be interesting to know if TB and USB-C HotPlug works with the ASUS Prime X299 Deluxe II onboard TTR controller ones SSDT-X299-TB3HP.aml is properly configured, like in case of the SSDT-X299-TB3HP.aml attached below. Anyway, please note that you need to use SSDT-DTPG.aml in addition to make SSDT-X299-TB3HP.aml properly work on your system
Concerning the Aquantia 5GB NIC, did you ever try the trick with 10.13.2 and the Aquantia "built-in" patch by Mieze, fully described in Section in Sec tin E.8.2 of my X299 guidelines?
For any further support, please provide complete EFI-Folder, "PCI" snapshot and IOREG-Save for your system in the X299 main threads. Snapshot's of your BIOS settings would be helpful in addition.
We will also have to adopt the XHC USB Kext for the ASUS Prime X299 Deluxe for it's use with the ASUS Prime X299 Deluxe II.
I do not expect further necessary modifications. Else, the ASUS Prime X299 Deluxe II should be fully compatible with all guidelines for the ASUS Prime X299 Deluxe.
I count on your collaboration and ask at the same time for your comprehension that I cannot provide help and support in threads different than the X299 main threads, which simply exceeds my personal capacities.
Good luck,
KGP