wow. those tranny bearings are pretty resilliant. i ran a tranny with no gear oil (dry as a bone) for a good 7,000 miles or more till they finally gave up. the only thing i can think of is that the input shaft is not 100% parallel with the crank, maybe a factory surfacing problem on the bellhousing or the motor? possibly if the engine block was hit hard on the edge the tranny case may not be sitting perfectly flush against the block... i dunno man.
also when they rebuilt it if they didnt properly shim the bearings then it will cause premature wear, but 20k is still a very short lifespan for a dealership rebuild...
and as for warranty i wouldnt know anything about that one lol.

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