Can you please describe what the drivability issues are? We have this on both our NSXs, as well as dozens of customer cars with out drivability issues. The standalone engine management system is literally a clean slate which requires proper tuning to achieve not only good performance, but good drivability as well. Also, please note factory traction control can be maintained on the 1995-2005 application. For your year & a basic supercharger system, we feel the F/IC is the better solution. If variables begin to be introduced (intercooling, turbocharging, etc) or your tuner simply prefers a stand alone engine management system, we then feel the Series 2 based solution is the best choice. As always, feel free to give us a call to discuss.
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The idle strategy is maintained by the factory ECU in both the Series 2 EMS & F/IC. So, stalling issues caused by a clutch would be the same no matter if the Series 2 or F/IC is place. I'm surprised to hear this was an issue however since we've installed our lighter weight clutch/flywheel in OBD2 drive by wire NSX. As you mention, the factory ECU's ability to recover from a stall can be caused by clogged air ports, so this should be checked.
Regarding traction control, to use the factory traction control, all factory sensors (including both primary and secondary O2 sensors on both cylinder banks) must be maintained. I believe the AEM traction system is the better solution for boosted cars however, which requires programming and setup to enable.