With the basic design of an inline 6 cyl,
it's hard to make a manifold that feeds all ports very well.
So for all out performance gains,
the individual throttle setup is the way to go.
Look at Igor's 6 cyl, 2.9" throttles per port.
If you want to just drive around, then you run lesser manifolds with lower power potential.

And if you plenumize the runners so as to run a maf sensor, you are limiting total performance of the engine as the cylinders/airflow is now very confused within the plenum, just look at the firing order of the average 6, the cylinders will be fighting each other for air within the plenum.

As for using speed density, that's the way to go with the system that I'm designing.To use a map sensor with ITB's is a waste of time, just opening the throttles a little bit will lose vacuum fast, but this is why they(ITB's)can make big power, less restrictions to power output.

You will want to source vacuum from each port(small lines) and group these together for power brake vacuum etc.

LHP