I thought I might mention firstly, that I use forums very regularly; however, this is my first post.
I am not sure if I had the exact same issue, as it last happened a few months ago. But I built a custom computer with the same motherboard an Intel chip and I believe I had the same issue.
I noticed that the RAM timings were not set to the values printed on the physical RAM sticks - after changing the RAM timing to the suggested values the crashes have ceased to occur. However, while running a stress test (Prime95) 2 cores out of the 12 failed after 2 hours, while the other cores were fine after 12 hours of Prime 95 (Can't remember if it was a Blend or Small FFT's test, I believe it was a Blend test).
No crashes or any other issues have occurred since I have changed the RAM timing (Except the 2 cores failing during the stress test)
I have an NVidia Quadra 4000 with 32Gb RAM.
But I will now attempt to overclock the CPU - the issue with the 2 cores failing during the stress test may limit my ability to overclocking. Since I cannot revert back to the previous default RAM timings as I will return to the crashes and kernel failures I may have look into compatibility of the Sabertooth X79 motherboard and Intel 3960x chip as you had mentioned you had narrowed the issue down too.
Have you received the replacement chip yet?