As for the throttle issue that's a good one considering you have replaced the TB. The foot pedal is responsible (obviously) for generating the command output to the PCM for actual throttle position. If you were to datalog actual position and commanded position along with RPM it may shed some light on your throttle issue, or at least be some benefit to someone better versed in that area. There are a number of items in the Drive by Wire and Throttle Body sections of the Live-link Gen II datalog PIDS to choose from that could be used to better look at the TB system as a whole electrically.
I have been learning from my tuner about shifting and how it works in the newer mustangs (11-14). The PCM has two things it looks at when making a shift. The MPH for that specific shift and the RPM. RPM however trumps all in the shift, so therefore if MPH is not met and RPM is it will shift as I understand it. Further the shift has to be anticipated by the tuner which takes some time to dial in many 6R80 cases. Better to sneak up on it than set it and then hit hard rev limit. We finally have my car shifting between 7100-7300 at WOT in 1-2,2-3,3-4 shifts. To do that MPH shift had to be massaged as well as toying with the RPM shiftpoint. If you log the commanded shift and compare it to RPM when you see that actual shift take place (along with MPH) you will see what I am talking about. Though the shifts are electronic there is still the mechanical motion of the solenoid fighting against pressure that has to take place in order to make the shift. That causes a delay. And the faster you go the earlier this has to be anticipated. Lund hopefully takes time to explain things like this with you over the phone as my tuner does. IT helps to better understand what is happening.
A third item in the process which will effect shifting as well overall is tire rotation per mile. This needs to be set correctly to begin with or shifts can be too high or low regardless of what the tuner does in the other settings. This can be also used to raise or lower your shift points while at the track if needed by increasing or decreasing the rot per mile value in your SCT tuner against the calculated rot per mile your tire is. (Assuming the tuner leaves that option open for you in your tune). Example - you are running a 325/45/17 MT DR, and the rotation per mile is 725. If you wish to lower the overall shift points of the car at the track you can lower that number to say 720. If you wish to raise overall shift points you raise that number. Trust me it works. Just remember to change it back if you are driving the car home so it properly recalculates the speedo.
last if you don't have a vacuum boost gauge I'd get one. Vacuum is a nice thing to know when problems begin to arise with age. Then you know if you are wasting time with smoke or other means of seeking out vacuum leaks.
Hope this helps. I'm still learning and I ask tons of questions from my guy every week.
Keep the thread updated. I'm interested to know you resolve since I am running a 14 auto as well. Never know when a similar related item may creep up. AND NICE ET BTW! WOW!
