Since it's a brand new computer your problem is likely drivers or firmware - it's especially important to note that the software they ship with the hardware is usually notoriously out of date, especially for motherboards and chipsets, which is probably where your problem lies. So basically go around the interweb and download the latest firmware for your mobo, bios, chipset, and latest drivers for your vidcard, any associated mobo controls, sound card, and whatever else you've got. Should fix you right up.
Switching to a SSD solved my microstutter when the game first came out, but it was similar to how you described - more of a visual game-pause while the assets loaded from the HDD.
It causes a conflict with nvidias adaptive vsync(almost all game level vsync with driver level adaptive does). You should have one or the other on but not both. In his case since its intel he needs to use in game because theres no driver level adaptive.
