I don't know if it's the case in your scenario, but I had hells own job getting the haltech to like the toyota sensors (dizzy to be exact), and it ended up that my tuning issues (similar problems to you, but ignition only problems) were directly related to bad inputs from the motor. Despite the fact that it 'appeared' to be the ecu at fault, it was infact the engine giving noisy inputs to the ecu, and the ecu spitting out bad output back.
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