Um, first, let's get this right, please. It's X79. Not X78.
And yes, I do know the difference between PCIe 2.0 and 3.0. It's about the encoding method used(8b/10b vs scrambling), and the speed of the interconnect.
PCIe 2.0 runs @ 5 GHz, and PCIe 3.0 @ 8.0 GHz. X79 itself doesn't use PCIe 3.0, at all, BTW. Just the IB/IB-E CPU support PCIe 3.0. The Intel X79 Express PCH is a PCIe 2.0 device. I think YOU are not sure what the differences are.
Also, Intel states that 2.5 GT and 5.0 GT are supported, and the SB-E processor is CAPABLE of UP TO 8 GT.
http://www.intel.com/content/www/us/en/processors/core/core-i7-lga-2011-datasheet-vol-1.html
Again, board is not the problem...CPU is. To properly test the difference, you use the same board for the platforms that offer it, 1155 get a board, and 2011 gets a board. You change CPUs, enabling real PCIe 3.0. Comapring the difference between differnt CPUs will only tell you the difference of the PLATFORMS, not the PCIe protocol used. You are missing my point. You don't need to test current/past platforms...the countless reviews published today already give you those numbers.