The MTF itself is off. So you'll have to turn adaptive off and go back through it and rescale it.
There isn't a limit on flow per se
, but when you rescale the MTF you will decrease the accuracy as the upper limit of flow increases. You can not go over 5volts (4.9x actually).
So work from your upper limit and go down from there.
Also be sure you upped the flow limit of the MAF in PRP, MAF --> Scalar --> MAF Maximum AD Counts, stock is 980 and you want to change this to 1023 (which is 5 volts).
My current MFT vs stock:
You can see that in stock form the resolution is greater around the 400 count area, which corresponds to highway speeds and light acceleration. Ford wanted a lot of accuracy in that area because that's where 75% of your time is spent.
The problem as I see it is, the ECU doesn't go point by point when looking for the MTF, it goes by an algorithm. If the scaling in not uniform or the ranges go up and down, the algorithm becomes more complex and this take more CPU power to compute. This is why I rescaled mine so the ranges are all uniform. Though I can not prove this plays any part in speed or accuracy. I can however prove that the space between the points, the fueling is predictably accurate, which to me means the algorithm is very close to perfect.
But, go back through your MTF and re-do it. Don't worry about any limitation on part throttle tuning, as in don't limit yourself to 400 counts and all after is for WOT tuning. That kind of mindset only works if you haven't doubled or tripled the max flow of the engine.
I do part throttle scaling up to 600 counts and I have no issues with rich conditions or the ECU thinking I'm asking for a different throttle mode than I really am. 500 counts and under 70% throttle I want to be near Stoich and that is what the ECU shoots for.