For the storage tests, we ran our (bare) Secondary SSD, a Patriot Pyro SE 60GB through three separate benchmarks, AS SSD, ATTO, and CrystalDiskMark. For the USB tests, CrystalDiskMark was used to measure the transfer speed of our Seagate GoFlex Desktop 2.0TB USB 3.0 hard drive.
We see a roughly 4% advantage in 6GB/s testing from the Gigabyte X79-UD3, and nearly identical performance in 3GB/s speeds. In terms of absolute values, and the rough error margin of our tests, these results would seldomly be recognized in normal usage, and even in the most intense applications would be difficult to tell apart. We see the Deluxe version perform slightly better across the board, but nearly identically to the P9X79. The additional Marvell SATA ports on the P9X79 Deluxe do quite well in read, but is the slowest in write speeds, which is probably why these are ideally labelled as the "SSD Caching" ports, being read-optimized.
We also see a slight advantage for the Deluxe over the base P9X79, but the Gigabyte X79-UD3 bests them both with an 11% write and a 10.3% read advantage. The speeds with USB 3.0 Boost slightly edge those of Gigabyte's "boosted" USB 3.0 speeds, but for all practical purposes, they're essentially the same.