I'm pretty sure I've answered this (not sure if it was to you or not but...). The best way to go about an upper/lower IM, is to get with either Synolimit or Synergy and have them port & port-match the components. For example [on my car], I had the manifolds (upper outlet/lower inlet) port-matched to each other. Afterwards, he ported the upper manifold inlet where it meets the TB outlet as much as he could without ruining where the gasket seals... from there, he port-matched outlet of the billet adapter that comes with the EPS TBs to the inlet of the upper manifold (and he double-checked that the outlet of the TBs were matched to the inlet of the billet adapter).
I'd say for an N/A car, this would be the best setup. You "should" be able to substitute the Motordyne/Z1 manifolds and have the same done to them, although I'm not sure how the Z1 is ported but I know the Motordyne is not. The results may change, or may be the same. The AAM manifold hasn't been shown to make or lose power (or do anything as far as anyone can tell), and neither has the RJ Mfg GTR conversion so your best guess is as good as anyone's for aftermarket manifolds.
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