Apexi' NEO tuning/general tuning advice

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What specifically is your issue with the idle? Do you have a wideband installed? Is the ECU running in a forced, full time open loop mode (I don't recommend it with the Toyota TCCS systems)? Leave the bypass screw on the AFM alone, you don't need to use it in conjunction with the NEO.

Unless the ECU is put into a constant open loop mode (can be accomplished via a few different methods) the ECU will work to adjust the idle AFR on its own just as it does during low to medium load engine operation. This is closed loop mode. The only time you can manually affect the AFR without the ECU fighting you is when it's operating in open loop mode. Open loop mode is engaged when the engine is first warming up, throttle is at 70% or higher (I think it's about 70%), or there is a fault with certain components such as the O2 sensor... These are your tuning windows. Any tuning of the idle AFR will need to be done when the engine is in open loop mode. Tuning should be done to keep the cold idle AFR at about 13:1. Don't try to stray from the ECU's normal operation when it comes to tuning idle, cold operation and closed loop operation... just tune it so the ECU doesn't have to work it's ass off and so the two systems will play nice with each other.