i'm gonna make some guesses here.... you need to do this
i did this on my wifes GTR that had a missfire when up it in third. the second part might be that your tuner may not have done your accelerator correction, or it could be your TPS. make sure your tps is reading the correct voltage at idle i think its 0.45v-0.55v at throttle closed position, the voltage should increase to somewhere between 3-5v at WOT. you don't need to do this with the car going but just the ignition turned on.whats your ECU ? can you datalog?