I can't give you a precise answer to this question because I've never used a 3-D simulation to design my intake runner and plenum.

But, again: I highly advise you to ditch the 3-D simulation for now and start working on a 1-D simulation ASAP. All your questions will be answered with it.

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If your intake valve start opening when you piston is almost at TDC, will you want the peak of your reflection wave pressure to still happen at this moment?