here's a thought:

1 mainboard per side, on hinges, boards 'facing' into the middle... fan on the bottom and the top with a blow hole on the top. place the drives on the outer sides, one per side to space out the heat. if you could put a colling agent in a ring around the top and an air channel down along the outside, the cooled air would go across the drives, under the bottom lip of the main boards then up through the middle across the cpus and grfx cards.

the power supplies and UPS i would probably put in the base.

you could also put vents along the bottom, about level with the bottom of the mainboards, to pull in air from outside... but if you have a proper cooling system pumping air from the top ring, it wouldn't be worth it

overall, i'd imagine stacking the parts by their heat production... hottest to the top

sounds like an interesting project.. can't wait to see it