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You didn't mention what scheme your system uses to determine air charge, ie: mass air flow sensor (MAF), speed density (MAP) or alpha-N. Assuming it's not MAF (because MAF would be overwhelmingly complex and ridiculous on a stack system), keep a couple of things in mind. Speed density systems require a manifold absolute pressure sensor. This needs to be a common plenum. So, with a 4 barrel throttle body, the MAP sensor is just a tap off the intake plenum. However, for a independent runner system, all the independent throttle body vacuums need to be mechanically averaged in a common plenum. This can be done, and there are several people on this site who have nifty systems fabbed up underneath the intake manifold. My opinion is that these complex plumbing systems generally result in a rather noisy MAP signal, although like I said, that's just my opinion. With an independent runner system, I think using an alpha-N scheme makes far more sense. The ECU calculates air charge based solely on RPM and throttle position. It's not so much fun to tune, but once dialed in, it works well.
I opted for a 4 barrel system.
Hope this helps.
phil
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