Just a thought, but are your stock wheels running the factory 305/40-22 tires. Any variance in tire size will not let the tranny shift at the right time under WOT. Front tire soze may affect this as well? Are you running 17s or anything up front? Anything other than stock?
You need to also verify your VSS( speed sensor) is reporting to the PCM correctly by using a GPS of some sort ( phone app, TOM-TOM, Garmin,etc) that will report your correct MPH and compare this to what the PCM is seeing! A few MPH off will do the same thing.
Personally at the track I experienced the 390s not letting me shift from 2nd to 3rd without barely letting outta the gas, then throwing the stockers on and shifting fine within about 20 min of each run. I later did the same thing on the smaller 325s and the same problem. Put the stockers back on and no issue. It's very obvious the difference in tire diameter.
Also, in your tune ( if tuned) if your rev limit is set to 5900 and your shift setting is 5950-6050(example) then you will hit the rev limit before you can shift and have to let off TPS to get the shift to occur. The opposite is if a tuner adjust the rev limit but not the trans shift points, then you won't reach your engine rev limit before the shift. It will shift too early. Now this is from Ford and GM tuning and from talking with a few Dodge tuners, the DCM computers are very similar.

Soooo..............if you are tuned, have your tuner bring your shift RPM for 2-3 shift down a few hundred RPM so you can make the shift. I believe the negative effect will be when you put the stocker tires back on, then at WOT it may shift way too early.
Just my .02
Scott
EDIT: John Hennessy engine controller????? Do you have access into the PCM and can you adjust parameters yourself?