Couple things I have not seen mentioned, but thought I'd point out/see what others thought.
First, if you have variable valve timing, the intake runner length should become a much less important variable. Its why the S2000 just uses a honking big intake, and why Honda's in particular respond so well to exhaust and improved intake packages.
Second, back when we all ran side draft Webbers at the track, the manifolds had vacuum logs on them. It was a 1/2 to 3/4" dia pipe that connected the runners below the throttle plates. With the carbs it was to make them less balance sensitive, but we also tapped any needed vacuum off of them. I wonder is a log with check valves would help balance the vacuum signal off the throttle bodies so you could centralize a vacuum signal?
Thoughts?
Dave