Aaron,
At this point, your guess is as good as mine since you're running standard calibrations. What this means (in a nutshell) is that you're running the exact same tuning that any of PHP's customers with a 49-state emissions 99.5-01 automatic are running (probably at least 1,000 others).
If others were to have issues similar to yours, we'd have some basis to go off of with what needed to be changed in the standard calibrations.
It's weird that you're having issues with our tuning but not stock or with tuning from another vendor, but my question is this:
Do you have a way to read scan data (particularly the exhaust backpressure data)? The PCM calculates torque (and subsequently transmission pressures) based on this reading. If you have a sensor/wiring issue or a plugged feedback tube, the PCM will default to pre-mapped tables and will make the necessary adjustments based on stock power levels. On a 49-state truck, the check engine light will not turn on in most cases.
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