I’d suggest going back to the basics then.
When you say “Clean Install” to Sierra, did you totally format (wipe out the drive) and reinstall the OS?
You have absolutely no VST instruments or anything else in your project except for 32 tracks with EQ?
I’m running a MacBook Pro with a 4-Core processor and though I’ve experienced the same issue; my system configuration is obviously different from yours. Anyway there have been many similar reports in general regarding 12-core processors.
Steinberg has also posted some articles stating that their products may not yield the performance levels you’d expect with Multicore processors and particularly on Macs.
But what are your audio settings in Cubase and what version of Cubase are you running?
Did you have any signs of this issue prior to moving to Sierra?
I know you said you tried all the Audio settings but have you tried the following settings?
Activate ASIO-Guard - ON
Activate Multi-Processing - ON
ASIO Guard Level - HIGH
Try setting the Audio Processing Precision to 64-bit if you have the option
Lastly, what is the exact version of Cubase you’re on?