So, an update:
I decided to revert to Yosemite for now. It's disappointing but when previously working HDA.kext patching in Sierra suddenly started to fail during startup I felt I had to draw the line.
I did "backport" several of your changes into my Yosemite install though Shilohh, among other things I changed to the MacPro6,1 system definition.
I also replaced the old DSDT and replaced it with:
SSDT-0 (with your various fixes and tricks)
SSDT-1 (Nvidia Drivers gave me a ~10% performance boost over Sierra with Apple drivers, no AGDPfix needed to load)
SSDT-4 (for a KT4004 4-port USB 3 card)
Plus a generated SSDT-9 for power management. (included a replacement of the X79X86.kexts in S/L/E)
Not sure, maybe I can use the SSDT-8 USB-fixes on Yosemite too? I haven't tried it yet.
I gained a more compatible system definition, I threw out GenericUSBXHCI (finally) and thereby future-proofed the install some more.
All in all maybe one step back and two steps forward.
A few things remain; like testing a migration of the custom kexts installed in S/L/E to the EFI-partion, but I am concerned as to what the cause for the audio issues are since my current install used your old HDA-patching method which was based on PikerAlphas-variant, not Toledas (I might misremember that). Perhaps it's more reliable?
My fear is that the audio issues will return if I start moving the kexts around and/or change patching method.
Oh well, that's in the future.
Thanks for the awesome guide and Happy New Year.