Quoting prove_it:
You'd still use the cyclone butterflies to improve the low end respond and torque curve. With a larger plenium though, you'll increase the top end and that's it. The cyclone manifold would stay the exact same, just with a bigger plenium for high end air flow. It's really the best of both worlds, now if only he could built a taper plenium instead, maybe make for better flow, and better cylinder distribution.
*edit: forgot to ask, but when increasing the size of the plenium with a cyclone manifold would the runner opening time change? I know most cars on the dyno like to have the butterflies open around 4100, but would a larger plenium shift that number higher?
Theoretically, yes. The larger plenum in this case is using the same "floor" of the IM, just "raising the roof" to increase the volume. What this does is increase the distance between the runner opening and the opposite wall, changing the amount of time it takes for a pressure wave bouncing off a closed valve to travel up the runner and ricochet off the opposite wall and then back down the runner, cramming an extra bit of air into the cylinder. I bet if you threw that manifold on the dyno and did back to back pulls with the butterflies open and butterflies closed, you'd see a different ideal crossover point compared to a stock cyclone IM.