Runners have, or should have, a design rpm range in which there is a VE boost caused by pressure wave resonance. Runners should also be designed with as few pressure losses as possible, meaning as straight of a shot into the combustion chamber as possible. I think it makes more sense to design runners with those criteria in mind, and then adapt a plenum.
If I were putting so much effort into designing an intake manifold I would be working with an ITB setup. IMO, it would be easier to get right and you'd get better performance in the end.
I don't mean to sound harsh, so take it for what it's worth. More power to you if you keep this up and get a nice design out of it.