I can see how a larger throttle body can affect the granularity of the throttle input - turning the pedal into more of an on/off switch than a linear input. Unless the TB is comically oversized I would think you could account for that in the tune
I can have MAP >= 100 anywhere from 30% to 100% TPS depending on gear/boost targets/etc. I have speed density working perfectly - alpha-n would probably break my car.
Can you post logs of the stumble when using SD?