Kozuti is SPCR Recommended and the smallest cooler I can think of, so only choice I can see here. Reference coolers have been nothing but miserable in my experience.
Scythe specs say the Kozuti is 110 x 103 x 40 mm. Assuming it's symmetrical, that is 110 / 2 = 55 mm and 103 / 2 = 51.5 mm from the CPU centre, respectively. The short side faces the RAM slots (i.e. cooler is longer sideways).
Edit1: ignore prior math, wrong figures.
Edit2: redid the math. The mini-ITX board is 170 x 170 mm (not 150 mm), and the picture I have puts this board at 890 px across, so 170 mm / 890 px = 0,1910112359550562 mm/px. I'm not sure about this mounting scheme, but I PRESUME the centre point is centre of the CPU's area in the socket. From this point, there is 54 mm of clearance to the second RAM slot, meaning the Kozuti MIGHT fit, but you can't use the first RAM slot. The bottom edge is not a problem, since there is 70 mm of clearance that way.
It's a tight squeeze overall with a "flat" cooler.
PS. Out of curiosity, I measured the GA-H77N-WIFI using the same method, there the sideways clearance is 59 mm, so the Kozuti should definitely work with just 1 RAM stick.
Case: FD Define Mini
Parts: P8Z77-M Pro µATX, i5-3570K @stock, N650Ti-1GD5/OC, G.Skill 2x4/1600/CL9 DDR3U, Xonar DX, WD G 1 TB, m4 128 GB, RX-5300 PSU
Cooling: Noctua NH-U12P SE2 + Scythe SS PWM, 2x Noctua NF-P12
Extras: Eaton UPS, Dell 24" EIPS, Ducky kb, SteelSeries m, Synology DS213j NAS
idle & load: CPU 32 °C & 44 °C @ 300/600 & 600/800 RPM, GPU 35-65 °C @ 1200-1650 RPM