If there was a restriction in the intake anywhere (from airbox to throttle body) then manifold vacuum would actually increase at high rpm - the engine would be trying to take in more air than the...

I just took a quick look at your main VE table and it has a lot of peaks and valleys. I would work on smoothing that out. For example, your 1200rpm line goes 51-55-50-57. Also your 100KPa line has...