Just like a rear end ring and pinion when they get worn and the factory backlash specs go out of whack, they make noise.
New carrier bearings and races moved the ring gear back into spec and the noise of the rear end goes away. 2 full trips back and forth to Florida and is still rolling fine > no noise.
Same with your transmission, you have 2 different generations of parts that you are trying to match up. Gears are cut in different machine shops and different years and are off just enough to make noise.
Tear it open and get in there with the Yellow gear backlash paint to see the wear pattern mating surface of old parts to new.
Bet you see the Heal Toe contact patterns are off to an other than ideal position.
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