Ok I will add my two cents worth as I agree your Stepper motor, Primary TPS and ECU are a wee bit out of sync. It could be they are or were in tolerance and tolerances are there to allow some further tweaking. I suspect when you get off the throttle and she dies it is because of the stepper motor being fully retracted or retracted wee bit to much in which the idle speed cam is retracted more then it should be verses the TPS and actual throttle plate opening engine rpm, timing and a multitude of sensors I do not fully understand. (I bet the main throttle plate opening has a tolerance when it is set during assembly also).
This sounds like a lot but Tweaking is all. It is like balancing the throttle bodies, how particular you are?
This is why when your bike is surging at idle it is searching for the right combination needed to idle if the TPS is out of synch with the stepper motor then the ecu has to compensate. I suspect this is not as easy even thought it is a computer. It has to compare throttle location verses rpm, TPS position, timing. Get this closer and I bet you will find some if not all of the popping you feeling in you seat goes away also. I see where your telling it to dump fuel at a certain position and oh right after that lets change the the ignition timing right after I dump the duel and cut off the air. I wonder if this causes a larger ignition event during valve overlap when it is not needed. O does the TPS being out change the ignition cell for the better or worse.
Ok more then two cents and I am starting to think out loud
I do think it is just some adjusting on the sensors and playing with the tolerances they allow.