I see you have a 2006 with a 5.4L.
Well, for 3rd gear, the only different apply component for 3rd gear operation is the direct clutch. It is used in 3rd and 4th gears. You mention a "whining" sound. This can be either stripped splines on the friction elements or a possible unseating of the snap ring that holds the frictions in the drum.
Either way, a flush WILL NOT fix it. It is broken.
The problem with a transmission that shifts too quickly is that hard parts (like splines and one way clutches) really pay for it. The friction elements really love quick shifts. Like DJ said, it's a real trade off for shift feel vs. longevity.
There is a VERY GOOD possiblity that over-running certain apply components during a shift (and shifting really quickly) caused a reversal of rotation that was just too much for a mechanical part to sustain too many times. I see it a lot with forward sprags in 4L60E transmissions when people "rock" their vehicles when stuck or shifting to drive while still rolling backwards out of a parking spot or driveway.
In any case, I think you have exceeded the mechanical limits of your transmission by high RPM full load shifts with too much TV pressure.
Sorry.
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Tuning, PCM flashing, and burning chips for 7.3s since 2008. Repairing all aspects of 7.3L Powerstrokes for 25 years.
Eight 7.3L PSDs in the driveway including a 1994 Crown Vic and 1973 F100/2002 F350. Looking for the next victim.
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