[NoDOHC]

CFD software is outside my experience, but if it is capable of simulating the flow in the manifold accurately (assuming that it is given good data) you have an excellent opportunity to maximize your learning as you go, while using the resources that you have to their fullest potential.

As you said, you do not have the typical toolbox.

Helmholtz tuning works for any level of boost (it is basically the natural frequency of resonance of the fluid system). The speed of sound varies with density of the charge, so you will have to that into account on the Helmholtz equation.

You can write the Helmholtz equation most easily in terms of the resonance frequency (First equation) Solved for L gives the second equation. This expects a uniform cross-sectional area for the runner, as any changes in velocity will create additional and possibly conflicting pressure waves.

(a = speed of sound, V = velocity in the runner at time of wave excitation, L = Runner length from source to plenum, A = cross sectional area of runner, f = frequency of resonance (which is related to engine speed, obviously).
I hope this helps some.

With the tools at your disposal, this should be one awesome manifold.

The offset sinusoid expresses the chamber volume as a function of E-shaft rotation (the period is 270 degrees, the amplitude is 20 in3 (327 cc) (654 cc peak to peak). Taking the derivative with respect to time requires that the x axis be in time units (pick an engine rpm). This will give you the rate of change of chamber volume with respect to time, which should give you a good velocity characteristic (given port cross-sectional area). Hopefully this will be good enough input data to get a reasonable approximation of how the manifold will flow.

Keep up the good work!