For example, with throttle cut, would the diverter valves be re-cycling air back into the intake? If so, how does that affect IAT's, boost levels, and compressor efficiency?
Also, if the manifold pressure sensor is detecting higher that requested boost (which triggers the ECU to cut throttle) more frequently with the IPP's than the stock IC's, then can we not assume that boost levels in your tests are not equal. If that is the case, then I think (and I may be off-base) that you guys should have done some logs with IAT and boost levels for a more fair comparison. Otherwise you are comparing temps for two different boost levels, which give an unfair temp advantage to the intercoolers running lower boost (i.e. stock).

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