To start off I am in no way a trans builder. I have rebuilt a few 4l60s, 80s and 42res, but never an allison and if my trans shit the bed, I would take it to someone who will BUILD it. And just a guess as I don't know the allison that well, sounds like a pump whine to me.
Like mentioned above no one was there to know what you have or haven't done. Wether it be assembling the clutch packs or slipping seals. I know you have your pride you want to hang on to but if I were in your shoes I would pull it and have someone more knowledgeable than myself take a look at it with you.
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