Hey mJolnir, I'm going to preface this with saying I haven't gotten to toy around with an ecoboost Mustang, with that out of the way heres where it looks like you're hitting limits:
Load Limits mJolnir.jpg
The part pedal seems to 'clip' with your current load, on the 2.7L F-150 in the stock cal that limit is set to 3.0 air load, so I've never seen it pop up.
The combustion stability you're getting is because your manifold charge temps are getting pretty high (especially on the second pull) and you're weighted heavily on the 150 degree row. You either need to let the car cool before doing the pull, or raise the load limits in the 150 row.
The last limit you hit on your second pull was the speed limiter, you can change it under speedo -> limiter.
Also consider logging throttle position and wastegate duty cycle. They'll give you an idea when you're reaching the limit of the turbo, or if you have a 'hidden' limiter coming into play.
Hope those help, let us know how it goes.