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None of those mods are radical enough to render the ECU unable to control the operation of the engine. To me it sounds like there is too much overlap dialed into the cam timing and you may need to play with them and adjust them properly, the 0 mark on the stock gears is no longer good enough for higher duration cams, it will still have overlap because of the longer duration and the extra time needed for the valves to fully close. Make sure that the 2 water lines under the TB are connected and also make sure the timing is set correctly, both can affect idle after warmup.
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