Might want to try the V8 tune, that has been around for some time.
Gonna ask some stupid questions here:
1. You are running 93 gas, right? E0, E10? Winter or summer fuel?
2. When you say flush, did you actually flush the trans, or do a drain & fill? Motorcraft Mercon LV or some other fluid?
3. When not going WOT, there's no stutter? Engine/trans warmed up before going WOT? What are the surface/ambient temps in your area?